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There is a open CAR00050982 for this resolved in 9.0.00 Fix Pack 3. The External Programs settings are stored in the <EM Install dir>\Data directory similar to version 7.0.00 in a file named ExternalPrograms.xml. Try this and see if it works,.
CAR00050982 has been resolved in version 9.0.00 Fix Pack 3
With additional testing I found that the ExternalPrograms.xml file is written when users exit the client.
This meant that if we applied the file to a citrix server that had active clients, it was overwritten when the users logged off.
By draining the sessions on the citrix server before applying the changes we were able to apply the settings successfully.