mysql - merge two large instances to one server (40GB of binaries)
The right answer depend from - what is Your full task description?


is it 12 different databases, which just need to have on same
server? 
is it the versions of same databases and You need merge data    in
each table?


in first - You still can use mysqldump, and it will be fasted method without additional steps and/or packages

if size of single dump is big - make dump by single database, table

user#&gt; mysqldump db_name table_name &gt; table_name.sql


Single huge file now must not be a problem with most of OS, but could be difficult for edit.

In second case, need analyse merging logic
simples way - mysqldump with --no-create-info (not CREATE TABLE), but could be problems with duplicate keys.

If some duplicate keys (indexes):

or edit dump (for big files - use sed) and change insert to INSERT IGNORE or UPDATE ON DUPLICATE

or create ETL Job with any of available package and manage merge logic.