Well if you do it in a careful way, it would have no side effects.
1) Make sure the anchor attribute is absolutely unique in the SQL Table.
2) The Anchor attribute should already be populated in the CS.
3) If you plan to change the relationship mapping in the Synchronization Rule as well, make sure the attribute is being populated both in MV and the Portal. That will ensure that the connected objects remain connected.
4) Always do a Full Backup of the FIM Service and FIM Sync Service Database prior to doing such things.
5) Never RUN auto jobs to do the run profiles right after doing these kind of changes, always go for manual execution of RUN profiles and always RUN the export RUN profiles AFTER you have made sure everything is going well. Once everything is fine, you can
then enable the auto jobs again.
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