Hi, I have this same issue, and was hoping for clarification. In my case the canon files are named for example, C0001.MP4 and the corresponding raw recorded on the atomos is named NINJAV_S001_S001_T001.MOV. So they obviously don't have the same naming convention.
Does anyone have advice on the best way to proceed? the ideal goal would be to remove the raw from the working drive as it's taking up too much space. And edit with the canon files and perhaps have Premiere make proxy files from those. But I want to ensure smooth linking to the raw for the online edit.