Are you sure it's asking you if you want to uninstall it? That really doesn't sound right. If you manually run the updater from within the UDA subfolder of the game, that should run it properly. On OSX, GOG.com made a change that caused it not to run automatically. But I wrote all the code for the autoupdater, and there is definitely no code in there for uninstalling anything, so either it was something that you read slightly wrong, or it's not the autoupdater I coded, or something mysterious.
In terms of the GOG.com version, I have gotten them new full builds that are fully updated to 1.004 and which are split apart by OS, and which include the 64bit Linux libraries. Previously there was some confusion caused because I gave them one build that had all three OSes in there, and only 32bit Linux, and so some things got messed about a bit with the updater specifically. I anticipate that they'll have the new versions up tomorrow (because of the time zone difference, it was well after hours when I got them the files today, despite it still being morning here for me), and either way that will resolve your issue both with getting to 1.004 and updating in the future.
I'm pretty sure that running it directly should solve it for you, though, in the meantime. Hope that helps!
