Just to be clear it was the MPLAB X environment that was used to program the emonth. If you want, I can find out the versions involved.
Ultimately I don’t care if you support it or not, I do see it as a paradox though, the manufacturers toolchain is not recommended. I understand the need to corral users into a manageable support route. The risk of course is you have just created your own protected branch.
I would say that (if does not already) the documentation should positively state that MPLAB X is not recommended, only because it is the manufactures development environment.
Using other tools is fine, but you do need to be aware of what’s already on the microcontroller. You can’t just overwrite and change things without taking that into account if the firmware you are uploading relies on those structures, no matter what the upload mechanism.
No worries on finding the version - OEM can only validate and support a handful of configurations as you’ve alluded to, for example, you originally said you were using Atmel Studio which is very different to MPLAB-X. A statement that just directly uploading with MPLAB (or whatever) is neither recommended or (officially) supported would suffice.
Hopefully you’ve seen that people are willing to help regardless, but it’s really difficult to diagnose problems off the normal path as there are so many variables to consider.