I don’t know if there’s a way to “ignore” a field when you click the duplicate button, it’s POSSIBLE a BPA Workflow hijacking the method (if any) that gets called when you duplicate to “null out” the custom field. (Similar to how you can use BPA to modify default values when you click the + button, but I don’t know if it’s possible to do something similar when clicking the duplicate button).
If not, you can always create a custom event or bpa workflow that reads from the custom field on all other work orders (basically in active_separate_cft) and throw an error out if the value already exists in another. (If you go the custom event route on insert, you’d likely need to make the event action an autonomous_transaction as you won’t be able to read active_separate_cft while you’re inserting in it, as the table would be mutating)
Also note that this would not read historical work orders so duplication of custom field values from historical work orders would also be possible. If the custom field has also been added to the entity HistoricalSeparate, then typically when the work order is closed the custom field value is also recreated in HistoricalSeparate, in which case you could read from there as well if you want to avoid that scenario too)