The strange thing really is, before your big update, everything went smoothly. Any ideas?
Yes: The update brought new features (like not synchronizing all events, but only since 90 days in the past), and many servers seem to be broken.
However, my personal strategy is to fix errors (or help fixing errors) where they occur in order to improve the whole ecosystem, instead of implementing hacky workarounds so that faulty servers don’t need to be fixed for the next 10 years, until CalDAV/CardDAV finally dies because there are no usable servers and clients…
Did you try to synchronize an empty shared calendar? If this works, you may try importing and synchronizing events in batches. Or maybe the OwnCloud logs can reveal the actual problem. Did you try to get OwnCloud support for that problem?