Measure voltage on 48 batteries at once using microcontroller
It's not easy to wire and fuse 48 sense lines to batteries.

When given a big task like this, with high numbers of anything, see if you can split the problem up into smaller bits. Both to get into terrain you might already know, and to shorten the development cycle with quicker milestones.

If you have a setup with 8 packs of 6 batteries, you can create 8 devices each capable of measuring 6 voltages. Each supplied by the pack they measure to remove complicated power supplies and noise problems.

An isolated CAN or RS-485 bus can communicate the measurements along to a master unit, or whatever you're measuring for.
Such system is easier to scale than one big board with 48 analog inputs, and perhaps already for sale or available through OSHW.  

This can keep individual stack units simple, as 6 to 8 is within the common count for ADC input channels. Whilst powering it from the cells themselves eliminates the need for complicated differential or isolated measurements.
Using an isolated communication channel removes possible fault currents, if any, from flowing between units or to the master.

You could prepare the unit to be able to sense more than 6 batteries. Or add a PTC channel to measure 6 series PTC thermistors to detect overtemperature in the stack.