The best way to deal with this situation is to contact the customer (they would not be considered as your employer) and figure it out. Get them to file a corrected 1099-MISC if needed.
If that is not possible, you can report what you feel is the proper amounts, in which case you will need to attach a statement addressing the change in the way you reported the 1099-MISC and you must be ready to supply documentation to support your case when the IRS inquires about it.
You will need to print and paper file (mail) your return with an extra explanatory statement.
Again, I would contact the person/entity that filed the 1099-MISC. Explain that you are going to dispute the 1099-MISC they issued and that because of this the IRS will scrutinize both your books and their's. It could be an honest error in which case they will simply issue a corrected 1099-MISC.
https://pocketsense.com/dispute-amount-1099-misc-8373403.html
https://ttlc.intuit.com/replies/5442014
