These aren’t modules tailing to load - they are config files that aren’t available and are (therefore) disabling the loaded modules. If you want to not load the modules, you need to set them to noload.
I’ve got servers running in call centers that have multi-hundred day uptimes, so the stability of the FreePBX system isn’t really an everyday issue. To me, what you are describing doesn’t sound like a FreePBX problem - it sounds more like hardware to me.
I’ve seen this problem before on other systems. On one, it was a typo in a config file that wasn’t caught during boot-up (which isn’t a problem any more) and the others were all bad hardware (a bad CPU in one machine and bad RAM in the rest). Could you run a low-level system test (like a stand-alone RAM test) and see if you are getting a stuck bit or something is losing it’s mind when it gets hot?
Another place to look would be in /var/log/messages and make sure you aren’t getting any hardware errors (CRC errors on a drive, for example) that might contribute to the machine losing it’s mind.
Also, as noted: ‘fwconsole reload’ should be your first choice for refreshing the system. The second is ‘fwconsole restart’, which will stop and start the server. The first shouldn’t dump your calls but might not solve your problem. The second one will dump your calls and probably solve the problem temporarily.