Could be that you need enable the Preserve Global IDs environment setting when exporting to fgdb. Assuming that you are joining on globalid and parentglobal id fields?
You could also set up the join in desktop before exporting.
Hi, this option does not exist when exporting the Feature layer via AGOL
If you use Export button in the service page it will preserve them.
Yes this is why using globalid is actually a poor choice. I know the help docs say different but they assume the data never moves. Plus the bugs with upper and lower ids in different products will get you too.
I have a write up on this here https://community.esri.com/t5/arcgis-collector-questions/related-tables-for-offline-data-collection/...
If you will be exporting you need to manage your own IDs - using a meaningful one or copying the globalid into a static GUID field.
Hope that helps
this is more important than I think Esri has given attention to.
Unifying cases between Enterprise and AGOL for GlobalID is both simple to fix, a foreseeable design issue, and impacts nearly all customers.