Some googling turns up a few old bug reports involving missing troops in VC, like this one: https://steamcommunity.com/app/48700/discussions/0/142261352654211033/ . That is a few versions ago, but see this second report and the VC devs response here for recommendations regarding reinstall and clearing cache when another player reported missing troops: https://steamcommunity.com/app/48700/discussions/6/1483232961039537328/
Though if that glitch is still present, it must be very rare--I've never had any disappearing troops myself, nor have I seen any reports of others experiencing it except for when I googled the above old threads.
If the linked recommendation doesn't fix it, the one other thing to check is any text tweaks you have done. Text tweaks are an inherently risky process, especially if you use the old posted ones, since most of them are from many versions ago, and small changes to some files can scramble some numbers elsewhere. Moreover, since you are playing Balance Mod, and those text tweaks that are posted were made from vanilla VC, there is a chance some mod changes have changes what some numbers should be, which can also cause unexpected behavior. You could revert text tweaks and see if the issue reoccurs in a new game, if not, then you could try to identify the problem tweak or simply switch away from text tweaks altogether and use Kalarhan's great Tweaks Tool instead (which is completely safe to use and can recreate most of the effects that people posted tweaks for).