That indeed was a tricky one to find.
It seems that the index of the project is also saved into the toe file itself. When switching from an evironment with increment filename activated into one where it is disabled (and also the create file link is disabled), touch will open the project with the index when opening the source.toe (source.toe => source.1.toe ).
Esp with create file link disabled this creates a big issue, as making changes to the project will only be saved into source.1.toe, and not into source.toe). So nest time we open source.toe, all changes we saved are gone. We would have to open source.1.toe directly to get the saved data. When we now save the project again it will override the source.1.toe but not the source.toe even though we opened it.
Reporuduce:
Create a project with Increment Filename in the Settings set to on.
Save the project as source.toe
Save again to create a fileincrement.
Disable File Increment and Filelink
Close TouchDesigner
Open source.toe
Will be opened as source.1.toe
Place operator and save the project ( Ctrl + S )
Reopen source.toe
Placed operator is gone and file is named source.1.toe
Hotfix: Reenable File Link seems to update source.toe and source.1.toe
We just took over an installation implemented our own logic with our project file which had Increment Filename Enabled. Changes were undone when the project was restarted for that reason. But now we know 