I don't know man, although I'm getting the exact same message I have had so far absolute zero problems with backup/restore and eventual new (BWS) modded installation. I'm also using the latest BWS version with GoG Baldur's Gate I, II. All I have to do after the restoration of my BGII folder is to manually delete the content of 'Temp' folder, otherwise the installation get stuck at [creature offset checker] right in the beginning.
It installs everything correctly, just be sure to apply latest hotfix for item revisions (Beta 1.13 - Jul 17th 2012) , spell revisions (Hotfix 01 - July 16th) and also extract (and overwrite) the newest version of BiG World Fixpack (11.1.3) and BP-Balancer (v0.33e) after BWS extraction.
Tested with full recommended/tactics hybrid install (without DSotSC) with 0 warnings/errors result.
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