Why are there Sample Limit Transactions from a losing Sample Limit record appearing as unmerged after an Account merge?
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.
CRM Help Documentation: Account Merge Administration