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You can look at writing a custom script, there are a number of support docs addressing this issue:
Is It Possible to Export to Excel From Data Load Workbench If Rows Are More Than 65536 records in FDMEE Version 188.8.131.52.220 (Doc ID 2470578.1)
How to export Data on FDMEE for more than 65K in Excel sheet (Doc ID 2481216.1)
There is also an example custom script in the community section of Oracle support
FDMEE: Export to Excel - "Reached export limit"(3949882)
Thank you so much.
Will check and update.
Another issue is that when we filter a data set in workbench, export to excel functionality/button does not work. We are checking this with Oracle as well.
Yes this was our exact issue. Thanks alot.