Most likely, it has nothing to do with the cleaning up but with something in the original file that was loaded. I.e. QCAD 3 would not have been able to save the original file directly after loading either.
I was finally able to get a hold of a file with that problem. If you do have another such original file that can be used to reproduce the problem, I would highly appreciate if you could send it to me via e-mail. Thanks.
PS: For the time being, please use "Save As.." instead of "Save" and always choose a new name.
Good practice for file management of a project called "MyProject" (applies for any software):
- Create directory "MyProject"
- Copy / create your file in that directory, e.g. "MyDocument000"
- After every significant change, save as new number, e.g. "MyDocument001", "MyDocument002", ...
This protects you not only from software malfunctions but also provides a persistent undo and a history of the file in case a wrong decision s made at one point or something is deleted and then later needed again, etc.
Alternatively, a version control system can be used of course.