You'll probably have to open a case with Sage.  They haven't shared details on how those encryption keys work, for obvious reasons.

Did you want to have one company in one install or two separate companies within one install

The want all of the company codes from both accounts in the new install.

So in the new install you want the various MAS_??? folders for both installs in the new install?  Easy Peasy. Just create the same company codes in the install as are in the old install. Then active each company and let the system create the files. THEN copy and paste over the old copies into the new install and convert the data. 

BigLouie,

Normally that would work, but what about the encrypted PII data?  Will Sage 100 automatically update the company specific encryption keys, and encrypted company data, for use with the different system files (and different system encryption key)?

There are also issues with UserKey mismatches between systems (for the audit trail), and you need to manually coordinate the data dictionary (UDF / UDT settings in the copied company codes need to match the target system exactly)... but that wasn't asked, so presumably it's already on the agenda.