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Prompted to Save Changes on file created with EPPlus

I am creating a series of Excel Workbooks using EPPlus v3.1.3. When I open the newly created files, if I close it without touching anything it asks me if I want to save my changes. The only thing I've noticed changes if I say "yes" is that the app.xml file is slightly altered - there is no visible difference in the workbook, and the rest of the XML files are the same. I have tried both of these approaches:
ExcelPackage p = new ExcelPackage(new FileInfo(filename));
p.Save();
as well as
ExcelPackage p = new ExcelPackage();
p.SaveAs(new FileInfo(filename));
and both have the same problem. Is there a way to have the app.xml file output in its final form?
The reason this is an issue is because we use a SAS program to QC, and when the SAS program opens the files as they have been directly output from the EPPlus program it doesn't pick up the values from cells that have formulas in them. If it is opened and "yes" is chosen for "do you want to save changes", it works fine. However, as we are creating several hundred of these, that is not practical.
Also, I am using a template. The template appears normal.
What is particularly strange is that we have been using this system for well over a year, and this is the first time we have encountered this issue.
Is there any way around this? On either the C# or SAS side?

What you are seeing is not unusual actually. Epplus does not actually generate a full XLSX file - rather it creates the raw XML content (all office 2007 document formats are xml-based) and places it in the zip file which is renamed to XLSX. Since it has not been ran through the Excel engine it has not be fully formatted to excels liking.
If it is a simple data sheet then chances are Excel does not have to do much calculation - just basic formatting. So in that case it will not prompt you to save. But even then if you do you will see it change the XLSX file a little. If you really want to see what it is doing behind the scenes rename the file to .zip and look at the xml files inside before and after.
The problem you are running in to is because it is not just a simple table export Excel has to run calculations when opened for the first time. This could be many things - formulas, autofilters, auto column/row height adustments, outlining, etc. Basically, anything that will make the sheet look a little "different" after excel gets done with it.
Unfortunately, there is no easy fix for this. Running it through excel's DOM somehow would be simplest which of course defeats the purpose of using EPPlus. The other thing you could do is see the difference between the before and after of the xml files (and there are a bunch in there you would have to look at) and mimic what excel would change/add in the "after" file version by manually editing the XML content. This is not a very pretty option depending on how extensive the changes would be. You can see how I have done it in other situations here:
Create Pivot Table Filters With EPPLUS
Adding a specific autofilter on a column
Set Gridline Color Using EPPlus?

I ran into this same issue using EPPlus (version 4.1.0, fyi) and found adding the following code before closing fixed the problem:
p.Workbook.Calculate();
p.Workbook.FullCalcOnLoad = false;

How to paste a specific range from one excel sheet to another as Paste Special - Linked Picture using C#

I am trying to including a table or specific range from one sheet into another sheet as an image/picture.
In Excel it is done by selecting the entire table from sheet2 and then on sheet1: Paste Special - Linked Picture.
Is there a way to get this done using C#? I am developing a project which requires this task.

I'm not sure about converting the contents to a picture, but you can read and write to/from a spreadsheet using the Open XML SDK (link). I've used it to manipulate Word documents, but I imagine it functions similarly for spreadsheets.

Paste-Link Excel ranges into C# app

I am writing a C# app where I need to paste/link tables/ranges from existing Excel documents.
Functionality that I am looking for is this:
user can select a range of cells in an open Excel doc and do a Copy
user switches to my C# app and does a past-link ... my app shows the table from Excel.
user can edit the source Excel doc - this does not automatically get reflected in the C# app. But I want to provide a Refresh button that when clicked will update the C# app based on the latest data from the linked Excel sheet.
I have figured out how to do a basic copy/paste. I cannot figure out how to do this paste-link. Please note I do not want to ask user in my C# app for any cell ranges..I simply want to do paste-link of what is already in the clipboard...
Any ideas if this can be done...it is all Microsoft so I would be surprised if it can't be.. but I am a C# novice.
Thanks for all input.

I figured it out. Here are the steps.
User copies a range in Excel sheet. It goes to Clipboard in a number
of formats but CSV and ObjectLink formats are of particular interest.
In C# app, trigger a Paste-Link function (this is any button).
Retrieve data from Clipboard using ObjectLink format. This comes out as text which contains:
Excel version identifier
Path to the excel file
The sheet name and the selected range in R1C1 notation
Save the ObjectLink data in your C# app, we will use it later as part of refresh
Retrieve the data from clipboard using CSV format. Parse it out and present in C# app. I converted it to HTML since this is what I am building
Modify the original source excel file - change something in the cells that were part of the original range - save the file.
Go back to C# app, trigger Refresh functionality (this is any button). IN your code do the following:
Using ObjectLink data saved in step 2, open the Excel sheet in the background using Excel Interop API tools. Select the sheet and range. Copy the range programmatically to clipboard.
invoke the same copy from clipboard as used in the last step of 2. Basically get the updated Excel data in CSV format from clipboard and replace the original representation you built during step 1.
This works like a charm although the COM part of opening an excel doc from C# is a bit slow I have to admit.
I have not found any references to this procedure on the net...works for me like a charm.
Cheers.

How to work with .xls file in C# application

In a C# console application I have a PointF[] array. I need to draw those points in an .xls chart file, but I need guidance how to do this?

Have a look at Open XML SDK 2.0 for Microsoft Office
I've used it before to do something like you're describing.
I started off creating an .xls file in Excel that had the correct chart which read values from a specific range of cells and so on. Then using the SDK I added/changed the values of those cells and saved a new version of the file. So basically I used the file created in Excel as a template that I could change whenever without changing the code (as long as the values are written to the same range of cells).
You could also put the value cells in a separate worksheet so that the user does not see them when opening the file...

How to Highlight Row in XSL file without Opening EXCEL using C#

I have an XSL file that I am generating from CSV from and Object etc. etc.
Everything is done except that I need to highlight particular rows in the xsl file. I don't want to have to open Excel and use Macros.
Is there a way to do this in C#?

Do you mean XLS and not XSL?
If so, here's a link that explains the basics of how to use Excel as an object. Since you're opening it as an object, it won't be visible (unless you want it to be), but you'll have full access to navigate, highlight rows, and do whatever else you would normally do in Excel. When done, dispose the object.
Connecting to and navigating Excel through C#