In our situation we worked with Esri professional services and discovered that our caching was too long between two hosting servers and a file share server. We used powershell to set the cache on both hosting servers to (see below) and that fixed our problem
Set-SmbClientConfiguration -DirectoryCacheLifetime 5
Set-SmbClientConfiguration -FileNotFoundCacheLifetime 2
Set-SmbClientConfiguration -FileInfoCacheLifetime 5
Since we do not have a high availability cluster, we eventually decided to go down to one hosting server and put the shared files from the file server on the single hosting server.