Logic errors after Updating from an XER Import

I have found that after importing an XER file to Update an existing Project some logic changes occur. These have lead to loops, which hightlighted the problem otherwise I may never have discovered the logic changes.

Has anyone else found this happening? Do you know what causes the problem? How do I avoid it happening?

The only way I can trust an import is to replace the existing project but then I loose the filters on Project Codes.