Hi,
The fact that you used Global CS instead of UTM zone 13 is not a big issue as you can easily convert geographic coordinates to plane coordinates with a tool such as this one
About the overall workflow, you don’t have to reprocess the whole survey in Emlid Studio because you already have points collected in FIX status, so the relative accuracy is fine for Pix4D process. You probably just have to process your base raw data, but that is just in case you need absolute accuracy. Have you read this thread ? You may find very useful information that apply to what you did.