It was fine some days ago and yesterday I noticed that now the bridge pickup has a lot less output now than the neck pickup, it's a pretty big difference. The guitar is a Godin Freeway Floyd with the stock pickups.

Does anyone know why this could have happened or how to fix it?

Here's a recording to show you the difference: https://soundcloud.com/nicocastro95/pickup-problem
It is quite common the neck pickup is closer to where the strings vibrate the most. If both pickups are the same output the neck will seem to be stronger. That is why bridge pickups are generally wound hotter.

Move your neck pickup further away from the strings.
It's not that, the problem started a couple of days ago, until then both pickups had a similar output. Check the recording I made the difference is huge
Well after hearing it it sounds like you have a shorted pickup. You lost quite a few windings on it. You will most likely have to replace the pickup. The insulation came off at some point on your pickup and two of the wires or more touched and in the process you lost a large portion of the windings on the pickup.
Well shit, I'd hoped I could fix it. I guess I'll have to start looking for pickups
You may be able to fix it. There's a chance it's the wiring at the control cavity, not a shorted winding. It could also be a pot, although usually that would give you odd spikes or scratching when working the knob.

I'd re-solder the contacts for that pickup, see if that gets you anywhere.
Pull the pickup apart and make sure nothing is shorting inside the pickup, happened to one of my guitars not to long ago. Separating the wires fixed the problem for me.