That is a matter of employment contract and applicable law, not immigration law. The USCIS fees are paid by the petitioner under the fee schedule; what the employer may recover from an employee is governed by the employment relationship and should be reviewed by an employment lawyer.
Government fees are the petitioner's; clawbacks are a contract question
Hypothetical example: a Rothesay manufacturer worries that after investing in the L-1B petition, relocation and two years of U.S. salary, the specialist could resign and join a competitor. The immigration side is simple: the petitioning employer pays the Form I-129 fee, any fraud-prevention fee and optional premium processing as set by Form G-1055, and those payments are made regardless of what happens afterward.
Whether the company may require repayment of relocation or training costs on early departure depends on the employment agreement, on New Brunswick and applicable U.S. employment law and on how the payments are characterized, and the company should take employment-law advice before including such a clause. Certain immigration-related fees may not lawfully be shifted to the employee in some categories, which is a further reason to get that advice.
The company should budget separately for the L-2 applications and for the eventual extension.