Update: Having cleared my computer of all versions of the BGs except the Deep Silver ones I then re-activated my Beamdog account and downloaded my copy of BGEE onto an external hard drive (something that I'd not been able to do before because of browser issues).
When I fired up the downloaded Beamdog version of BGEE it automatically picked up the saved games from the Deep Silver folders (which were installed from a DVD).
So, the downloaded version and the DVD version must be able to 'speak' to each other, on some level at least.
Thank you everyone for the update, and solutions. I run Windows XP on my laptop, and I've always run the mods through the Program file folder (though for some reason I still got weird errors despite BWS setup was supposed to clean that up, and avoid these issues), but I didn't know that was not recommended. Next time I'm moving the game to the root location instead.
Windows 8/10 is more restrictive than Windows 7 when it comes to it's OS drive (c:\), you can read about it at technet and clearly see difference when you use non-admin account, so don't install anything there even if some people telling you "it works for me".
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When I fired up the downloaded Beamdog version of BGEE it automatically picked up the saved games from the Deep Silver folders (which were installed from a DVD).
So, the downloaded version and the DVD version must be able to 'speak' to each other, on some level at least.
BWS setup can recognize this right?