Hi Esteban,
Yes, it is possible. However there is not an GUI option to do this.
Check the instructions in this post:
Be very careful with this, backup all your data before trying.
Other important points to have a trouble-free merge:
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Protocols A and B should be configured in exactly in the same way.
Right-click in the top node > Edit protocol to see the Protocol configuration -
To avoid overwritting Subjects, be sure there are not duplicated Subject names
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If Subjects use default anatomy, this default anatomy should be the same in both protocols
Best,
Raymundo