I'm still not completely clear on what the actual problem is.
I thought I understood that the issue was that the CPU wasn't 'seeing' a CTRIO2 module, and that replacing the base fixed that. If that were to happen and the I/O configuration were set to 'Auto', the CPU would have disconnected the CTRIO2 module config when it didn't see the CTRIO2, and then would have recreated a new empty config when the CPU was able to again see the CTRIO2. My original comment was just explaining that you can reassign a disconnected module config to the module, which prevents you from needing to touch the program.
To clarify, the H2-DM1E issue that tech was describing is fairly recent, not older units. The symptom is that in DC bases (more so than AC), some CPUs would struggle to start their power supplies. Once they started, they were fine, but some units would just keep trying and never get booted. We hadn't changed anything in our design, but apparently the P/S chip manufacturer did, and we were forced to find a workaround. That shouldn't have any bearing at all on module discovery.
So lets take the problems one at a time, and maybe it would be best if you contacted us directly. Send your contact info to support@hosteng.com, and we'll help you through this.