There is no safe storage in MM6, and the only safe storage in MM8 is in the backpacks of the characters lodged at the Adventurers' Inn in Ravenshore/Blood Drop. I think the chests in the basement of the Merchants' Guild in Ravenshore were intended to be safe storage, but it didn't work out that way.

Incidentally, are you sure that it was the respawn of the map that cost you your money in MM8? That should not have happened. I would have thought it more likely that it was caused by your sinking of the pirate fleet. The Regnan pirates take exception to the merchants hiring you to do that, and they immediately raid the Merchants' base in Ravenshore. And when they do that, the first place they hit is the bank. Well, if you were a pirate, wouldn't you?