Immigrant intent is explicitly not disqualifying for H1B.
9 FAM 402.10-10(A) (U) INA 214(b) and H Visas
(CT:VISA-1623; 09-29-2022)
a. (U) The express text of INA 214(b) indicates that it cannot be applied to H-1B applicants. In addition, INA 214(h) provides that an H-1B nonimmigrant may have "dual intent," i.e., the fact that an H-1B nonimmigrant has sought permanent residence in the United States or will be seeking such status in the future does not preclude him or her from obtaining or maintaining H-1B nonimmigrant status. The applicant may legitimately come to the United States as a nonimmigrant under the H-1B classification and depart voluntarily at the end of their authorized period of stay, and, at the same time, lawfully seek to become a permanent resident of the United States without jeopardizing H-1B nonimmigrant status. Consequently, your evaluation of an applicant’s eligibility for an H-1B visa must not focus on the issue of immigrant intent.
Suggest you speak to your company’s lawyer about the potential for the fee being charged, but it is supposed to be for new H1B applications only.