The fee applies only to new applicants, per https://www.axios.com/2025/09/20/trump-h-1b-immigration-visa...

"Section 1. Restriction on Entry. (a) Pursuant to sections 212(f) and 215(a) of the Immigration and Nationality Act (INA), 8 U.S.C. 1182(f) and 1185(a), the entry into the United States of aliens as nonimmigrants to perform services in a specialty occupation under section 101(a)(15)(H)(i)(b) of the INA, 8 U.S.C. 1101(a)(15)(H)(i)(b), is restricted, except for those aliens whose petitions are accompanied or supplemented by a payment of $100,000 — subject to the exceptions set forth in subsection (c) of this section."

See https://www.whitehouse.gov/presidential-actions/2025/09/rest...

Nothing in there says it only applies to new applicants.