I had the same problem just the other day. My battery died at the 98% completion level for an SBF flash!
Various forums seem to indicate that the phone will not charge via USB when in the bootloader. Other threads, such as
this one, seem to indicate that a wall charger might still work. For me, it did seem that plugging in with a wall charger for a while was able to put some juice back into the battery (I turned the phone off first). However, there is no good way to check the battery level while the phone is in bootloader mode, so I didn't trust that I really had a good charge.
I eventually ended up cutting the phone connector end off of an old USB cable, stripping the insulation off the end of the red and black wires (taped all other wires safely out of the way) and, using some electrical tape, fixed it so the red wire was on the positive terminal and the black wire was on the negative terminal of the battery (the polarities are marked on the battery; I connected to the outermost terminals --
don't connect to the inner terminals). Then, I carefully put the battery back in the phone with the wires still attached and plugged the USB cable into my computer. I used a second USB cable plugged from the computer to the phone's connection port to flash the SBF using RSD Lite. As soon as the flash was completed, I unplugged the rigged connector from the USB port while the phone rebooted. Once I knew the flash was successful, I pulled the battery and removed the taped on connectors. I had nearly a full charge once the phone was working again and I could check the level. Everything seems fine so far...
This method is not for the faint of heart, but I was desperate and figured I would get a new phone (I am eligible for an upgrade) before I was going to spend much money on an external battery charger (plus, I needed to get the phone working ASAP) Of course, it would be a lot simpler if you can find someone else with the same phone so you can charge your battery using their phone.
I take no responsibility if you fry your phone or cook your battery.