However, isn't this effectively bypassing the ground isolation of the DC converter? And if so could this cause problems / fry something?
Yes and yes. It depends upon what you're doing with the 48V source. What is your need for isolation in the first place?
Will I get inaccurate values from the analog input because of different grounds?
Yes, unless your voltage divider measurement is made relative to the same reference point (voltage is always relative!) as the Arduino's, you will get "all over the place" values. The easiest way to do so, as you've noted, is to connect the grounds together. This isn't always a bad approach, it just depends on why you need the two systems to be isolated.
If you absolutely need isolation you can use an isolating linear optocoupler as in this circuit:http://ruggedcircuits.com/html/circuit__24.html
The Rugged Motor Driver
: two H-bridges, more power than an L298, fully protected