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
Although this is an old question I can confirm that this is still an issue in the current version of Delphi 10.3 Rio.
The answer above regarding line endings
https://stackoverflow.com/a/53360447/6445054
Solved the issue for me I had imported some very old Delphi code which had CR line endings in a couple of places, as soon as I started moving code around the debugging broke completely.
The option to turn line endings on has moved slightly in Rio it's now ( Tools - Options - Editor - Source - Show line breaks).