We use zipped file geodatabases.
1. Compress the entire folder using the Send to> Compressed (zipped) Folder option in Windows. Make sure that the fgdb is not in use at the time.
2. Once the file is uploaded and published as a feature service (if you are planning to edit it online) make sure that it is shared properly.
3. Finally, if you are going to update the fgdb on the Portal, be sure to update the SERVICE and not the file geodatabase.