I freqently troubleshoot tsprofile problems by taking ownership and assigning administrators full contol without any ill effects to the user. Generally I do this to move large psts or delete corrupt links. The only problem I have seen is where one of our admins took ownership of someone's tsprofile using his own account (rather than local admins) and the user got an error loading their profile (it basically states that the user or administrators need to be the owner of the folder). As a rule, I give local admins ownership rather than myself (I log into the server using my account and it belongs to local administrator's group). If you have Domain or Enterprise level rights, you may find that assigning to the local admins is unnecessary (I don't have that option, so local admins it is!!).
Also, if you do end up blowing away their permissions, give the the user full permissions to their root folder (normally their network share) and force the permissions down. I do this on a daily basis without problems.