After forcing the closure with the Task Manager when I re-open SH3DI I get a 'recovered' file which is not the last state I left the file in.

The file for recovery purpose is saved every 10 minutes (see preferences panel), so its state depends on the moment the scheduler saved it.

Does the paid for Windows Store version completely overwrite the Source Forge version ?

No, and you can keep both versions on your computer, but as they have the same name, you have to pay attention which one you launch (even if they are compatible).

Does your problem happen also for a new file or a file created from a demo?