This is just your (un)educated guess or you really know what you are saying (i.e. you are electrical engineer skilled in lithium polymer technology)?

My uneducated guess is that it may work. At most batteries will not explode but be charged slower or to half capacity because you are sharing the current and each battery takes less (not more).

In fact the chances are high that it will just work because this is how it works with battery in Tapwave Zodiac. There is one long battery inside made by sticking two separate li-pol batteries together. Google for 'tapwave zodiac battery' and maybe 'dissection' or 'replacement'. There are also known issues when one of those two batteries inside becomes dead sooner, it will still work but the capacity becomes worse.