Yes, anytime a transponder is removed or replaced an altitude correlation between what the transponder is reporting and what is displayed on the altimeter needs to be performed. This is outlined in FAA CFR Part 91.413. This regulation indicates that following any installation or maintenance of a transponder where data correspondence error could be introduced, the integrated system has been tested, inspected, and found to comply with paragraph (c), appendix E. Furthermore, these references indicate that an integration test between the altitude reporting equipment and transponder system must be conducted.
For complete information, please refer to these FAA regulations or contact Southeast Aerospace Tech Support team at shop@seaerospace.com.