Hi Sam,
I've done merges. Typically, it's GL/AR/AP with supporting tables and posted transactions. The trick is to make the acct/customer/vendor lists unique just prior to the merge. Once it's all combined, you can use the Toolkit for Adagio to change or combine codes. For example, each GL should be assigned a unique department or at least a range that's unique. Again, the Toolkit can be used to prep the data.
Also consider the supporting tables. For example, a control account '1' might have different meaning in each dataset. You should review control accounts, bank accounts, terms codes, etc.
if you're interested, send me an email to work through the details.