The "incorrect" reboots should not hurt. Just do not let windows (if that is what you use) do a disk check on it. It deleted most of the stuff on my kindle one time, and created a bunch of .CHK files on my kindle.
Also, for a totally depleted battery, you may need to let it charge a day or more (green LED). You can get aftermarket batteries fairly cheaply.
Do not discard the old battery -- it can be repaired inexpensively as well (replace internal LiPo cell). If you are adventurous enough, check out the "
kindle battery surgery" thread in the dev corner.