You can deduct them both and report the refund as miscellaneous income next year.
Also, i have filed a 1040X for 2015 that hasn't finished processing yet,
but will have loss carryover deductions. Do I have to wait until the
IRS processes it, in order to file my 2016 taxes and carryover the loss.
Assuming you positively elected to carry any loss forward (instead of back), you can assume they will process it as filed or wait - the choice is your.
