Correct, as long as you lived apart for the last 6 months of the year, for the purpose of the HSA, even if she claims them they are still treated as dependents of BOTH of you.
There is never a guarantee that you won't be audited for any reason, however, you would not be in the wrong for paying the kids medical expenses with your HSA even though she claims them and you do not have medical insurance on them.
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