That is frustrating, especially with a dozen shortcuts to rebuild. I have seen updates reset custom search entries before, so it is worth checking the list before re-adding everything.
In Settings, go to Search engine, then Manage search engines, and look under Site search. If your shortcuts are still listed there, check whether they have been switched off and switch them back on one at a time, testing each with its keyword in the address bar. If an entry has vanished completely, add it again with the same keyword and the site's search address, using %s where the search term goes.
If they disappear again after a restart, it is worth checking whether an extension is interfering by testing with extensions temporarily off, and reporting it as a bug from the browser's Help menu with your Opera version included, since a dozen entries switching off at once after one update sounds like a regression rather than something you did.
