I encountered the same error; in this case it was caused by the fact that the object had been deleted while iterating over its list.
Even though the object itself was deleted, it was not deleted from the list. At debugging the object was still visible. When later in the process this object was referred to again from this list it could not be found in the database, resulting in this error. It was solved when the object was removed from the list before it was deleted.
I think it is possible that because of the object monitor is not committed yet the object will be deleted because of the long duration of the microflow.
It might be smart to look for ways to shorten the microflow time. You could also for example start the microflow with a create of monitor and commit this. Then create a sub micrflow that does the processing in batches, start up this sub micrflow in background with the java action from community commons. This way the microflow is run in background and in batches and you monitor object is always accessible.
Though Maarten's answer is correct and I would advise his answer it is still strange that the object is not there anymore. The object would only be removed if there are no processes using this object and that seems not to be the case. So I would also double check the delete behaviour of references to this object to see if this object is not accidently removed by some other proces.