There is a fix for invisible opponents (in flying fortresses) in the patch, as well.
If you really want that chest you can email your save to support@larian.com for them to fix, but it probably isn't worth the effort unless you run into additional opponents or traps that you can not defeat / bypass.
Someone who ran into a problem where Ba'al had a fast, over-power attack used CheatEngine to fix their hit points until they got past that fight. If you have the PC version you could do the same to try to get the chest, though someone using Steam reported that they can have a problem with CheatEngine even when playing single player games.
