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I don't know if this applies in your situation, but this is something that happened to me last night.
I had a semi-dormant site that was using 2.010. We recently switched servers, so I just backed the site and the database up with the intention of attending to it one day.
Last night, I decided to upload the site. I had forgotten what version of XOOPS it was, so I just created a database, uploaded my site and added all the updates I thought were necessary for 2.0.13. Needless to say, it didn't come out too well. It was a total mess with phpdebug errors out the yingyang.
I deleted everything except the mainfile.php, uploads, themes and a few html files I needed. I even dumped the database. (Of course, I had a backup of the original site.)
Next, I re-uploaded the original site with the exception of the files/folders I retained AND re-installed 2.0.10's core files from a copy I have on my hard drive.
Works perfect now and I decided to upgrade the whole thing to 2.2.4. I've got to do some work on the site, but none of it is related to the upgrade.
The whole process took about 3 hours.