Question:

Why are there Sample Limit Transactions from a losing Sample Limit record appearing as unmerged after an Account merge?

Answer:

Only records which have actual Calls with sample disbursement are shown as merged. Record updates may not be marked as merged.

NOTE: A Record update can be the Account merge process itself, which appears as a transaction. When the Sample Limit Detail Page is edited and saved, it appears as a transaction.

Related Documentation:

CRM Help Documentation: Account Merge Administration

Thank you