I'm wondering if I'm potentially causing any long term damage here. I've read all the threads on using another gas cap other than OEM and there are times where I have to (leave the truck at a small Marina and boat across a lake to a cottage, vehicle can sit for a week or more - people get gas stolen all the time amongst other things easily accessible so I don't need that). All I do is remove the OEM cap and install one from Napa I bought then I put the OEM one back on when I leave for home.

Presumably the system loses some pressure over the week and as soon as I fire it (after replacing with the OEM cap) all my idiot lights are on. Forgot my OBD reader this last weekend so I had to drive back without the use of cruise control too - the horror! But yeah, all the electronics getting disabled sure seems ridiculous and you would think after a full drive cycle, another tank of fuel, everything would clear. Nope - I have to clear the codes manually after each episode here and then all is well, or I suppose I could just keep waiting for them to clear on their own but even from this past weekend, likely multiple drive cycles and another tank of gas the damn codes remain until cleared. Stupid system.

Ok rant over... but should I be concerned about any long term issues to the Evap System? Anyone very familiar with the electronics that might offer an opinion?

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It's not like you're driving with the non-OEM one on there, so I can't see how you'd be doing and harm to it..While it's annoying and inconvenient, at least you have a workaround..