Can a flexfield qualifier be changed after it has been created?

No. Once a segment qualifier has been designated for a specific segment and has been saved, it will permanently have the attributes with that qualifier. For example, you accidentally designate the cost center segment as the natural account segment. Even though you do not compile this, the system saves the changes. And once it has been saved, it will have all the attributes designated for the natural account qualifier, even after it has been changed back, resaved with the correct qualifier and compiled. This is the inherent functionality of the software. Unfortunately, there is no real easy solution for this issue. The only option is to create a new chart of accounts and attach a new set of books/ledger.