I recently converted an HID canopy light to 4x 13w PL using Keystone CC1322MTP ballasts. After running it for maybe an hour, one of the bulbs turned off followed by another, then a while later they came back on. I assume this is due to some type of thermal protection and i've experienced it with other ballasts and fixtures in the past. is there any way to stop this from happening so I can use the fixture continuously?

Look for thermal mode of these ballasts. Usually, modern ones are marked with temperature ratings. A click of IR thermometer pointed to ballast case will give a clue.