Although re-linking is supposed to help with performance, in this particular case their customer has 3,000 users in the Source, but 170,000 users to match against in the target.
QUESTION - With all of that in mind, should we disable the re-link checking and would their be negative side effects that we should warn them about beyond sync times?
The initial sync will take time regardless of re-linking. Once the initial sync has completed the deltas should not reflect any significant time and if it is taking a significant amount of time then the interval should be shortened.
Re-linking really comes into play when profiles are reset or re-pull has been issued, since these actions remove data from SQL and result is full synchronization.
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