However, isn't this effectively bypassing the ground isolation of the DC converter? And if so could this cause problems / fry something?
Will I get inaccurate values from the analog input because of different grounds?
Yes and yes. It depends upon what you're doing with the 48V source. What is your need for isolation in the first place?
Do you think running a 1000W motor off that battery would be a reason to need isolation?
In other words, electrons going to and from the motor should never travel on the same wire as electrons going to and from the Arduino.
As long as you can keep the ground return path of the motor completely separate from that of the Arduino it should be OK, as the motor itself is an isolated device
No I got that.