Cool I'll have to check those tools out.
For now I just used a file renamer to prepend the subfolder name into the file names, then I used suction to pull all the files into a single folder, then I installed sketchup on a virtual machine and loaded & saved all 11k or so textures in one full swoop. Then I threw the files back into their subfolders and copied the folder into the main sketchup directory on my original OS. Everything is now loaded and works a charm, so looks like I should be good to go for a while
My main OS is due for a re-image, it's been a while and is getting buggy, just haven't gotten around to it, so it turns out that was the culprit.