Can a company with hold advance payments on a 1099 employee?

There is no such thing as a "1099 employee".   If you receive a 1099NEC then you are not an employee at all.   You are an independent contractor.    Why do you think you are supposed to get some sort of advance payment as an independent contractor?

https://ttlc.intuit.com/questions/2584365-am-i-an-employee-or-an-independent-contractor

Do you mean to take out federal tax withholding?

not sure what you mean by advance payments but as a person receiving a 1099 (indicating independent contractor) for whatever you did for the company may be a legal and not a tax question.