The residual energy in the AA cells is not valuable, the fact that the cells are portable, safe and cheap is.
That means using them for battery charging, that could use wall power, which is a few orders of magnitude more powerful and several orders cheaper (than full price batteries at least), is a total inversion of values and waste of time.
I too had access to a stream of partially used discarded AAs, and was able to make a steady donation of them to a charity serving the visually impaired, for use in their handheld illuminated magnifiers. They were perfectly matched to this service, as premature exhaustion of the cell was of no consequence to the users, especially given that they were free. The key here was a reliable stream, which allowed the service to abstain from buying full price cells.
If you insist on trying to recover the energy (I'm trying to imagine a desert island or post-apocalyptic situation where you don't have mains power, but do have the theatre's discarded AAs), then a) mixing AAs of a different charge state will result in premature run-down of the string of cells and loss of efficiency rather than damage (as long as you remove flat cells promptly) b) inverting up from a single cell is the least efficient way to do it, better to use a higher voltage and c) 18650 can be charged by a low current without reduction in life, as long as you continue to observe the normal charging envelope.
With a decent battery and charge-protect circuit it should be fine, since both the single-battery protection (using, for example, the popular DW01 chip) and charging IC (like TP4056) already limit the current through the 18650 cell; the current has nowhere else to flow, unlike the case with serial/parallel configurations.
If you look at the DW01 datasheet and it's typical application circuit (below), you can see that it actually monitors the current already and can completely disconnect the battery using M1 and M2 transistors in case of a failure. In parrallel and serial connected cells the IC does not monitor the currents between different cells and can't disconnect them from each other in case of a failure.
The temperature sensor, however, is still recommended for additional safety and redundancy, that is why some LiPo cells include a temperature sense output in their integrated protection circuit: for example, an external short circuit directly between the cell contacts situation could only be handled by a temperature sensor. This situation, however, could easily be avoided by designing a decent PCB and enclosure.
Best Answer
Yes you can put Li-ion cells in parallel, and yes they will charge, though they obviously will take longer to charge. There are many considerations (cell capacity, charge state etc) in putting cells either in series or parallel, but with only two cells I doubt many would be of concern to you. There are many 2-4P batteries in the RC community.
The only warning for you is to either fully charge or majority discharge (I always discharge on my Li-ion charger) your cells before connecting them together. Once connected together give them at least 15 mins to stabilize before attempting to charge them as a single unit.
You might read through something like this or many other good texts related to care and maintenance of RC battery packs to gain more knowledge.