What I did so far (by the way, for what it's worth, I am using WB version 306):
1. I deleted the "blank" patch.
2. Since in WB there was a problem with load order - it was "locked", so it changed back to whatever it was previously locked as - I unlocked it, ran BOSS, then locked it again.
3. I rebuilt the bashed patch I already had in place, without deactivating it in either MO or WB - it seems in this case changes are made to the already existing esp, since in Overwrite there was only a Docs folder with no esp, but a change I had made to a tweak (armour shows amulets) did seem to have taken effect.
Admittedly, I left the deactivated/merged esp's unchecked in MO - nonetheless, they sill showed as checked in WB's 'Merge Patches', probably because of previous rebuilds; also, at the start of rebuilding, I was shown a list of plugins - "mergeable, but tagged NoMerge" - to be deactivated, which I did not deactivate; however, I had left them active previously as well, without the double hair problem appearing.
4. I deactivated and deleted the bashed patch in MO, then rebuilt it again - with the merged esps still unchecked, and the NoMerge ones left active - this time there was an esp file in Overwrite, so I created the mod etc. as normally.
All the same, there is no change - things look as before.
Thus, first - would there be a suggestion what to do next, I'd rather avoid experimenting with checking/unchecking things hoping something works; second, I am curious about the NoMerge plugins - should they actually be deactivated prior to building the patch, and why, if they are not going to be merged - I looked through WB's readme pages, but there doesn't seem to be much on this specific topic there.