I think the chest that has your materials delivered to it would respawn. I have not tried to store anything in that chest. This is out by the workbench.
However, any chest that is in the home should be safe.
One thing I have noticed (or maybe it's just my imagination) but everything in Skyrim seems to reset faster since I got HF.
New patches and content can sometimes reset all the scripts that generate random encounters and such. It can even sometimes give you a multiple spawn battle right after loading the game up post patch. Those are always fun.