The two answers seem to be deliberately confusing?.
The more charged of the two batteries passes charge to the flatter one, until they are balanced - and as there's no current limiting high currents 'could' flow.
It's quite simple - they are perfectly safe to use in parallel, IF you do it properly - it's quite simple, use brand new batteries of identical type. You should never mix different types or makes of batteries, or old ones and new ones, either in parallel or in series.
Li-Ion batteries are supplied in a partially charged state, this is their optimal storage condition - and all should be pretty well identically charged. Often chargers for individual LI-Ion cells (often will accept 4 to 8 cells) can be set to charge/discharge cells to their storage settings, you could use that to balance identical cells that have been used individually - or you could charge them fully individually.