Microsoft has issued a warning in KB3161916 about a potential data loss scenario that can occur during public folder migrations. Before anyone panics, it's important to understand that this issue impacts public folders where…
…all your folders' replicas aren't on the primary database (the primary database server which the migration service connects to). All data which is initially present in folders that are being migrated are copied, but any incremental changes that are posted after the initial sync may be lost.
Thinking back to the public folder migrations I've performed in the field, they all happened to be for single-database environments. So this bug would not impact them. Similarly, for other projects where I've assisted in some way, the risk of data loss had been mitigated by adding replicas of all public folders to the databases on the server where the migration service was connecting.
For customers who do fall into the scenario in which this bug occurs, the risk is that any changes to data in folders that are held in replicas away from the primary server, or any new folders that are created on those replicas, will not be included in the incremental synchronization pass that is performed to complete the public folder migration. Microsoft explains the scenario in more detail here.
The fix for this issue is expected to arrive in Exchange 2013 CU13 and Exchange 2016 CU2, as well as be rolled out to Exchange Online in a similar timeframe. In the meantime, if you can't add replicas of all of your public folders to the server that the migration service connects to, Microsoft recommends you wait for the fix before completing your public folder migration.