It's not clear what years are involved here, but let's say the return with tax owed was 2024 and now she wants to file separately for 2025, which will result in a refund being applied to 2024 debt.

First -- she signed the 2024 joint return without looking at it?  Where did the 401(k) distribution go -- did she benefit from it?  In any case, she can request innocent-spouse relief from 2024, but that takes a while, and the result "depends" on many factors you can find with some research. 

For 2025, she is neither an "innocent spouse" or an "injured spouse."  IRS is going to keep the refund as long as she owes for 2024.  Best choice might be to file an extension and try to work out the problem by October.  Does the spouse intend to pay the tax debt?