OK, now I understand better; the problem is obviously coming from the re-gereration of the project by CubeMX.
Which version of CubeMX are you using, and which generation options have you selected?
With earlier versions of CubeMX (and possibly also the last one...) if you modified the project under Eclipse, CubeMX get lost and confuse things... In this case, the best bet is to save the .project and .cproject files before regenerating with CubeMX, then restore the saved ones before restarting System Workbench...
Anyway, if you don’t select new third-party components (like FreeRTOS) CubeMX should not modify the project, only modify source files. This is especially true with the last version of CubeMX if you generate the project in the root directory.
Sorry for the inconvenience,