Yes - You will need to file 2 separate 1099-MISCs one for the dates that the vendor was a sole proprietorship and one for the dates the vendor was an LLC.
IF the LLC is an SMLLC and treated as a disregarded entity, then you would only have to send one 1099-MISC for the new LLC using either the SSN or the EIN (since the entire amount will be reported on the person's personal income tax return on a Schedule C).
