Hi,
unfortunately there is not easy way to merge SEPMs, replication must be set up at installation time, not now. Set it up on existing installations was not a good idea as you have seen.
There are several things that should be taken in consideration like the complexity of your environment (policies, groups, etc.), what can be sacrificed if required, time constrains, etc. in order to accomplish your needs; unfortunately I cannot easily verify those things in a forum, I suggest you to come back to the support so they can further assist you via phone or remote support sessions (Webex) but explicitly ask them to reproduce your scenario in lab, test the procedures and come back to you with ins and outs before going ahead in your production environment with complex activities. Now you better restore your SEPMs at their last working status.
If you need something else, please send me the case ID so I can have a look at it.
Regards,