For anyone that may encounter similar issues in the future. It was discovered that while using the regenerate command through the CLI, it may attempt to force the Native Template to be upgraded to a version that is incompatible with the Studio Pro version being used (in my case it is 8.15.1 trying to install NT v6.0 which is for Studio Pro v9+)
When this happened it may have added an additional file to the patches folder that needs to be removed. In my case it was trying to add react-native-firebase+messaging+10.1.0.patch
What I did to solve was to remove the file, push to GitHub and replaced the Native Template with the correct version and I did this by opening the NB GUI where it prompted me to complete the installation.