I wish I had a good explanation for you, but I don't.  I think I followed what you were trying to say, but I'm not sure why there was a problem.  Even stranger is the fact that the compiler did not change 1.38 -> 1.39, so I can't explain it away with "the compiler changed..." 

I'm still looking into the best solution for multiple projects accessible from the IDE.  I have some ideas I'm prototyping.

I re-compiled one of my libraries.
The library is called [ioLibWin64].
The project option for the target name is [..\Libs\ioLibWin64.a]
It creates a .dll called [ioLibWin64.a].
I have checked destination folder, LIBS, and it contains the re-compiled .dll with new date and time.

My main project has, in its project outline list, the filename, [ioLibWin64.a].
Hovering the mouse over it shows it has the correct pathname.

Main project project-options also show, in the search-directories libraries list,  [..\LIBS]

Rebuilding my main project failed, however, because it could not find ANY of teh library routines in my compiled .dll library.

I removed [ioLibWin64.a] from teh project outline list, saved the project, then added the same file back again and saved the project.  It didn't help.  Re-build still failed.

I re-installed SF3.9.  Repeated attempts at rebuilding my main project all failed as above.
At various times during the above, I tried to CLEAN and rebuild.  No luck.

What eventually worked was reverting to my library, doing a CLEAN and rebuild, then returning to teh main project, doinga CLEAN, then a rebuild, and suddenly to my relief, it all worked again.
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John