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I have merged MPA programs into NATS and NATS into MPA, several times now. Moving backends isn't hard, and takes about two weeks depending on the program size, tools to move, paysites to resetup, ect. Both have tools to assist with converting links over, webmaster referrals, stats, ect. Most of the work is done on your part, resetting everything up, most of the backend is repopulated directly from the processors.
Moving any program backend won't ever go 100% smooth. You should never expect it to go smooth either.
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