Rename projects ..Does that work ?
From what I have seen this is a general problem with C/C++ under eclipse. Eclipse was written for Java where ther is no concept of cross compilation and different versions of header and source files for different targets. Versioning under Java was a nightmare until tools like Mave were introduced.
It is extremely frustrating in this environment to use a previous project as a template for a new one.
It also is a side effect when e.g. using a git repository as an intermediate between differnt development machines, some of which run under different operating systems. This often happens when a development machine is upgraded, replaced or stolen.
What is probably needed is a better make system (cmake or autotools?) and perhaps a move away from the java centric eclipse environment.
Embitz has a nice feature ‘Import recursive’ which would be a nice to have in SW4STM32 it does not presuppose any existing make instructions from another IDE, just looks at compilable files in the filesystem it is given.
Precompiled libraries would also improve things, this is something that SW4STM32 seems to be working towards. Any Brown (http://andybrown.me.uk) has worked in this area fro a number of years and has some very nice C++ libs, perhaps he could be enticed by ST to move and include support for the Discovery boards with graphics/touch screens and newer HAL libs.