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).

No, it is every time you petition. So every time you apply for the visa.