Is there any pattern to the timings when the check-ins stop?
If it is occurring right at midnight,.I’d recommend disabling the UpdateHistoricalCounts procedure as described at All Endpoints stop updating for a specific time of the day
If it is at some other time of day, it would be useful to check how that aligns to SQL maintenance jobs such as backups, reindexing, or consistency checks (DBCC).
If it’s not occurring predictably, I’d recommend opening a support incident and enabling FillDB logging.