From time to time I lose breakpoint functionality in Delphi.
I thought this to be a Delphi 2009 issue but now I have also it in Delphi XE.
In Delphi 2009 by
I had a related problem: I lost the breakpoints in a particular file, but the other files were fine. What had happened was that I had renamed that file, but unknown to me the DCU for the old file was still being used because it was being referenced in a "uses" clause somewhere.
The solution is to manually delete all the DCUs (doing a "clean" is not enough because the old file represented by the DCU is no longer in the project) and rebuild. You will get a compile error showing the bad "uses" clauses.
I solved my issue by making sure Debug was set to Local: