DnSpy adds changes I did not make when I Save Module

[PeteJobi]

dnSpyEx version

6.5.1

Describe the Bug

I made some small changes via IL edit to a program and saved it via "File > Save Module". It crashed. I tried investigating the crash but couldn't find it: happened too deep in .NET code. After some fruitless troubleshooting, I started again by importing the original program into DnSpy, and going straight to "Save Module" without making any changes. This new program crashed as well (when I get past a step by changing values during debugging). I checked the diff in a hex editor and to my surprise, there's tons of changes.

Why is DnSpy adding changes I didn't make? Is this normal? Is there a way to exclude changes I did not make when I patch?

How To Reproduce

I can upload the program in question if anyone asks for it.

• Drag and drop the program into DnSpy
• Go to File > Save Module

Expected Behavior

There should be no changes when I save module without any edits.

Actual Behavior

There are changes when I save module without any edits.

Additional Context

No response

[GazziFX]

This is absolutely normal, even without changes it will rebuild PE file and will remove all unknown sections and metadata streams, if you enable all toggles does it still crashes?

[PeteJobi]

What toggles? The ones in the Save Module window? Only "Shared Method Bodies" is checked. I tried unchecking that but it crashes too.