I've built an application that my company owns the code to.
One company wants a slightly modified version of this app (branding mostly) to distribute internally (using https://developer.apple.com/programs/ios/enterprise/).
I'm also going to sell it thru the ordinary App Store.
Would I run into any issues here? I can't find any information regarding that this somehow wouldn't be allowed, but I don't want to shoot myself in the foot here either...
Any insight out there?
Simple answer NO.
As far as Apple would see it - they would be two completely different applications. Each one would have a different App ID and a different provisioning profile.
You will however have to purchase an Apple Enterprise Developer license if you want to distribute through the Enterprise program.
If you have anymore questions just ask.