It's not likely you will be able to amend the return as a joint return as you would both have to sign it for it to be able to be processed. You can't amend a return to switch from married-joint to married-separate after the original due date of the return. You can contact the IRS and ask them if you can provide them with the schedule C you need to report the expenses associated with the missing income, but they may not be willing to accept that.
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