If you are getting 9V from two lithium batteries, then that is very very bad. Your protection circuit board (PCB) should prevent those batteries from overcharging, a max of around 4.2V per cell (8.4V for 2).
Are the batteries swollen? If so, stop using immediately. If they are outputting 9V, I wouldn't use them again either. They might catch fire or explode.
General rule: If you don't know what you're doing, don't use lithium. Know the warnings and drawbacks of the cells, and what to do in case something bad happens.
My work place is working with a company that uses lithium-ion batteries in an industrial setting, and I can tell you: this flax is seriously dangerous. Be careful.
