Hi cness.
Thank you for posting your question about merging customers; and thank you Mark for posting that you have a utility for merging customers.
Depending on whether HQ is being used or not, determines the steps needed to merge customers without causing other issues within the system.
There are a number of tables, besides transaction, that need to be considered when merging customers:
ShipTo
TransactionHold
Order
Journal
Transaction
NOTE: If there are ARs/Payments care must also be taken after fixing data in these 2 tables:
AccountReceivable
Payment
In addition, one of the merged customer records should be removed so that it can no longer be used.
The steps to perform the customer merge are not something that can be posted as they may need to be adjusted depending on your situation; and if you need assistance from Microsoft please open a new support incident.
NOTE: Always make a backup before running any update, delete or insert scripts.
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NOTE: Mainstream support for Microsoft Dynamics RMS 2.0 ended on July 10, 2016; and extended support ends on 7/13/2021:
community.dynamics.com/.../microsoft-dynamics-rms-2-0-mainstream-support-discontinuation-july-10-2016
support.microsoft.com/.../search

This is less than 6 months from now; and you can continue using RMS after this date but technical support will not be available.
I would recommend checking with your partner in regard to what they may recommend as a replacement system after the extended support end date.