Do not use merge in combination with snapshots. Merging two regions can cause data loss if snapshots or cloned tables exist for this table.
The merge is likely to corrupt the snapshot and any tables cloned from the snapshot. If the table has been restored from a snapshot, the merge may also corrupt the table. The snapshot may survive intact if the regions being merged are not in the snapshot, and clones may survive if they do not share files with the original table or snapshot. You can use the Snapinfo tool (see Information and Debugging) to check the status of the snapshot. If the status is BROKEN, the snapshot is unusable.
Is there any jira ticket about this issue? Or maybe somebody can describe in details the nature of snapshot corruptions?