Solved
Do we have to file separate or can still file joined? She also worked 3 months in FL and will be filing FL taxes as well.
First you will file a joint return. Then, since she is considered a FL resident just like you due to the MSRRA rules you will file a joint non resident VA return to get back the taxes withheld in error ... then get that changed ASAP for 2018. https://ttlc.intuit.com/questions/1899369-state-military-filing-rules
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