HI Tim,
Anything in the event logs that could point out issue related to the replication setup ? Ensure that each of the replicated folders has a unique root path and that they do not overlap. For example, D:\Sales and D:\Accounting can be the root paths for two replicated folders, but D:\Sales and D:\Sales\Reports cannot be the root paths for two replicated folders. So anything in the DFS health check via the DFS Management console?
If you have Microsoft support contact worth checking it and whether you will have to reset the replica and set it again unless there is a way around to fix this after repartitioning.
Hope this helps.
JS
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