As long as the music files are still on the player, deleting the database file simply forces the Clip to build another one anew.
Your “missing” files are actually “hidden” from view on one computer, as your Clip is most likely connecting in different USB modes on the other computer. The processor of the Zip can commumicate in one USB mode at a time, so files transferred in MSC, for example, won’t be seen if the computer establishes an MTP connection.
The purpose of the “Auto Detect” function on the Sansa is to increase your likelihood of establishing a connection. For most users, this is fine, since you can simply plug the device in, a connection is established, and you can transfer music. Problems arise when, unbeknownst to the user, one mode drops, and the device falls back on the alternate mode.
Once connected, the device should happile resume charging, unless the USB port cannot provide enough current for the high initial charge rate. This is why a USB 2.0 port is recommended. In theory, a 2.0 rated port can provide 500mA of charging current. we can run into problems using those handy ports on the front of your average desktop PC, since manufacturers really really love those winky (often as thin as 24 gauge) wires running from the motherboard to the front ports.
Try using a different USB port, I like to use a universal (longer, about 1 meter) microUSB cable, routed to the rear USB ports. Observe the battery icon,and see if it “rolls”, indicating active charging.
There’s one Achilles’ Heel in this equation: the processor in the Clip handles everything in one chip, the USB bus, processing, and charging. If the device is not establishing a connectin, it halts charging.
You can try using a smartphone charger, they provide plenty of current, and the Clip will charge without trying to establish a connection. This is because there won’t be any data on the USB connection (since it’s just a power source).
On the device, you can manually select one USB mode by going to Settings > System Settings > USB mode. Windows 7 includes Windows Media Player 12 which supports MTP. (Windows 10 and later support the mode).