If the redo had actually affected your chest, which I tested myself afterwards just to make sure and it did not affect the chest that I had placed nor the items in it, then there wouldn't have been any items left in it period. As you said yourself that items were left in it I can only conclude that someone must have taken the items out of your chest.

I noticed when I checked them after you reported this that you had someone cmodified onto your chests who could have taken the items out of them. Perhaps that will need to be looked into as well, because I am 100% sure a redo, which is what I did, could not have affected those chests in that manner at all.

Also noticed I'm missing my gold bars, iron bars and slime balls. About 9 spaces total which should be filled with items are now empty in my misc chest.

Update: Other missing items are a stack of nether stone and a stack of soul sand.

Sweet, thanks.

Update: 86MaxSmart got me my important stuff back, case closed