Yesterday Microsoft released an important Hotfix rollup package for MIM 2016 SP1, the build number is 4.5.286.0.
The main issue fixed is the following:
After installing MIM build 22.214.171.124 or 126.96.36.199, the ma-data objects are deleted and not recreated in the FIMService, causing all synchronization rules to fail. After installing this update, this problem no longer happens.
Both builds causing the issue are still listed but not available for download any more. But if you installed one of the above hotfixes I highly recommend to update to the lastest hotfix.
The issue was also discussed here: MIM Portal Sync Rules have become orphaned