Flair is not using the process information to monitoring the progress of a run (it would not work on a cluster system), but rather by checking if there is an activity in the output files. If for some reason there is no activity (no output message) for at least 2 minutes (configurable in the flair settings), flair shows the TIMEOUT message.
it doesn’t mean that the run has stopped simply flair doesn’t know.
You can always click on the Attach button and it will try to re-attach to the process