Managed to fix this via SQL Management Studio. There is no way to fix this via arcPro as far as I can tell.
Solution using SQL Management studio:
-Find the table which has duplicate GIDs
-Identify the duplicate GIDs and record them.
-use a command similar to this.
UPDATE [egdb name].[unm].[WATERJUNCTION] SET GLOBALID=NEWID()
WHERE GLOBALID = '(your GID(s) here)'
Lastly you'll have to delete the duplicated items manually in ArcPro.