I think it's actually per visa. I know the linked article says per year, but other sources I'm glancing at seem to indicate it's an application/renewal fee. Actually, it's not even clear that you have to pay again to renew after 3 years; it might just be the initial fee.

Based on the language in the executive order:

"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"

It sounds like it applies every time you leave and enter, provided you are a nonimmigrant alien on H1B (which they all are).