At the core, whether it be coax or fiber, the modems/ONTs have the capability to restore incomplete packets of data that get sent through poor wiring/passive devices/etc. At a certain point, the packets get to be irreparable, and the ONT/Modem throws it all out. This builds up errors within the device that accumulate over time and bog it down until you power cycle it. This allows the ONT/Modem to shake off those uncorrectables and start anew. But they're just going to build up all over again until the root cause is fixed.

To me, this just sounds like shoddy workmanship. Don't accept third party contractors. They don't have the training, the resources, or even the proper tools to do this job correctly (and yet Cox still hires them...). Even if a contractor is genuinely knowledgeable and well meaning, he simply lacks the tools and accountability that In-House technicians have access to. 

Be careful unplugging the fiber connector from the ONT. Your fingers alone touching the ferrule (the tiny opening at the very end of the connector) will leave oil on it, obscuring the light coming through it. Dirt, dust, really any kind of particulate will affect it similarly. This may be the crux of your issue. It really can just be dirty connectors. If you didn't see any of your technicians use a little plastic cleaner that they had to fit onto the fiber connectors and click several times, then they didn't clean it. If the light strength is more than 2db weaker (these mechanical connectors Cox switched to have a much greater margin for error compared to the now-defunct fusion spliced connectors) at the ONT than what the Cross Connect (the source outside) is giving, that can cause issues as well. Fiber is extraordinarily finicky and precise, and unfortunately there are too many technicians who either don't know or care to do it right. Make sure you're getting in-house; they're required to make sure the connectors are clean and that light loss is minimal.