ITS#8444 Do not clear the pending operation when checkpointing

When a checkpoint happens, if we remove the CSN from the pending list,
accesslog won't pass it onto the accesslog DB. But in a delta-mmr
scenario, an accesslog entry without a CSN faces a race where it might
be applied twice - that usually fails and causes a full refresh, other
times it can cause a silent desync - both are undesirable.