I replaced the files, just like normal. MB doesn't find my phone anymore. MB does find my USB drive, so it can read removeable drives, at least some of them.
I uninstalled MB completely, got rid of all evidence, %appdata% (both local and roaming folders), installation, C:\Users... etc. I couldn't find any other traces of the program, apart from the afore mentioned. Installed 3.2 as a fresh (as fresh as I can) install with no music added, and MB can't find my phone anymore. It will happily read my USB drive, but can't find my phone.
I updated to 3.3.6904, same thing.
After that, I dropped in the new files, version 3.3.6952. Same thing.
I tried uninstalling the drivers to my phone's USB and reinstalling to no effect.
Edit: So something interesting happened, after I used VSS to restore all the folders back to a version from last saturday MB finds my phone again. I'm at version 3.3.6940 now, with the restored version.
This new issue however persists, with version 3.3.6952, MB will not detect my phone.
tl;dr: when updating to 6952, MB doesn't detect my phone. Restoring the installation folder back to 6940 works in getting my phone detected by MB.
It is absolutely mystical how going to 6952; uninstalling MB; deleting all files (that I can find (though it seems I did NOT find all the files)); then reinstalling 3.2 can screw up the detection completely, even in older versions.
Good thing VSS exists.