Have you ticked / unticked the checkbox "All source editor units" ?
I don't think, now I opened the Unit Dependencies screen, and the default ins that checkbox is checked. I bet I did not uncheck it.
I understand that when checked it includes all units opened in source editor, even if they are not part of the project, while when unchecked it restricts exclusively to the unis which are part of the project. And this is ok for me.
I will check more to understand better what is kept into lps. I expect it to contain only the files opened durin last working session, not also files opened in the past.