My systems have numerous external data source references and we've never had to restart in order to restore the connection to one of them.
Where are the external data sources located? If they are on a system external to yours, is the connection to them reliable?
Have you checked your file for corruption? (Run a recover and see if any problems are found. Test the recovered copy and see if it has the same issue.) Best practice is to never put a recovered file into use but to replace it with an undamaged backup if you determine your file has been damaged.
Another "Best practice" bit of advice would be to not use your copy of FileMaker as the Host but to set up a dedicated machine with Filemaker or Filemaker Server installed on it for use as the host.