I've personally used WHMAutopilot for long time and I don't see any problems for its integration. We will assist you for its integration but let me remind you one thing about WHMAutopilot.
It gets slow and slow once you grow beyond 200 - 300 customers. Once you reach that stage then migration becomes painful but I think modernbill has designed some script for successfull migration from WHMAutopilot to modernbill.
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