what updates are you referring to? nothing that I know of is touching this file which means it should just work.

Sometimes after I reboot and do a repo sync and run cros_sdk it downloads the chroot again and clobbers my old one. It is possible it isn't unmounting properly or something. It looked to me like an update, but if there are not updates that would trigger this, is there a log for cros_sdk that might give some hints as to what is happening?

that's a bug.  the sdk shouldn't be clobbered unless you specifically told it to do so (e.g. --delete).

I haven't ever seen this myself, but what you describe sounds similar to  crbug.com/834412 

It indeed matches the description of the other bug. I will contribute there.