Let me understand the flow here:
1) You open a file in TextEdit let’s say.
2) Something updates the modification date in the background
3) When you save the file it says “The file has been changed by another application”
If this is the case, there isn’t much you can do to work around this because as far as the application TextEdit knows the file has changed from underneath it and it’s going to warn that this might be the case. I don’t think there is much you can do if you’re changing the document or it’s attribute while it’s been open with another application. You can actually reproduce this yourself by using TextEdit to save a file, use the command line to “touch” the file and then go back to TextEdit to make some changes. When you try to save this you’ll get the same prompt you’re seeing.
Please let me know if I’ve misread the situation here though, this is a bit of a stab in the dark.
Cheers,
Sam