Hm, tried first with comparing the lpi files from two related projects, where one has Run enabled, and the other not.
Many parameters different of course, but, focusing on those which seem to be potentially relevant, tried to bring them to match step-by-step.
No recognizable effect so far, regarding the enabling.
Then i backuped/removed the lpi file and tried to recreate it from the lpr file.
Drag/drop - how meant?
I did an 'Open with ...' of the lpr file targeting the lazarus.exe. Result:
I see my original project file in the IDE, but at first position additionally a very initial unit1 appears.
When compiling, it compiles to <drive>\Users\<username>\Appdata\Local\temp etc.
When doing 'Save project as ..', it offers a brandnew project1 with an project1.exe being generated then (exe!).
Same when (of course) telling the original project name as target.
With other words: by half a brand-new project will be created (i'd expected to save the existing project maybe as lpi, lpr, lps).
What might i have missed when trying to recreate the lpi file from the lpr file?
Edit: involved versions: Windows 10; Lazarus 3.6 64bit
Setting debugger backend to gdb instead of fpdebug: no change.