This particular chemistry in general is "less likely" to burst into flame because of the problem you've got, but none are immune to it, so be aware of that first.
Next, it is possible (likely) that whichever cells went too low will have either (or both) lower capacity than before, and less current delivery capability (more voltage sag under load), compared to how they were before.
If you're willing to accept that, and still want to try reviving it, you'll need to open it up far enough to reach the BMS and it's wires that run to each cell. At the connector on the BMS you can measure with a voltmeter from the main negative output to the first pin on that multiwire connector, then from that first pin to the next one, and so on until you get to the last pin, and measure from that to the main positive output wire.
Write down all those voltages in that order, and you'll have a list of the cells in the pack.
Probably it's just whichever cells are used to power the BMS (usualy the first few), so you can then manually charge each of those, slowly, until they match the other cells.
This can be done with a "lab PSU", which has both adjsutable voltage, and adjustable current limit. This is an easy way to be able to charge single cells of any chemistry, or even the whole pack if you get a PSU that has a maximum voltage high enough to do that. It can also be used for troubleshooting other electrical things, including ebike stuff like hall sensors or throttles, etc.
Or you can use a single-cell LiFePO4 charger, but most of the ones I ahve seen arent' adjustable, so those will simply fully charge a single cell as fast as they can. If you want to be gentle to the cells that are too low, this probably wont' do that.
There's other ways, too, if you look around at posts that mention single cell charging or charger.
Once youve got all the cells about the same voltage, and above whatever the BMS cutoff is, you can then just run the regular charger to fill up the pack, and then test it to see if it still does what you need it to do.
If it doesn't, you could replace the cells that were run too low, and probably fix it, or you can replace the whole pack.