I have had the exact same problem.
I went to all the shops in Phoenix looking for a battery for the cell because the present battery was totally drained out and would not charge again.
Finally, I landed up in a shady little cell shop. Got a Nokia battery with similar connector points and I was able to reflash my device.
The N900 has the BL-5J battery which is also used by the Xpress 5800. I got a BL4U. Note this is the smaller than the BL5J and cannot be used on a daily. But it is good to reflash.

Once that was done. I just had to recharge my original battery and I was good to go.

Moral of the story. Reflash only with a full battery. And if there is an issue do not wait for the battery to drain out.

It cost me $25 and half a day.