That depends on the written agreement with the acquirer and applicable employment law, not on the immigration framework. The official terms describe what is paid to the government; the company's recovery rights are a contract question to settle before any payment.
The government's terms and the employer's terms are separate documents
Hypothetical example: a Rothesay founder's acquirer proposes to pay the corporate amount under the official framework on her behalf and mentions informally that she would repay it if she left within three years. The official program page and FAQ describe the processing fee as nonrefundable and describe the gift and its treatment; they say nothing about what an employer may recover from an employee. That is governed by the employment agreement and the employment law of the relevant jurisdiction, and it should be negotiated and written down before any payment, with legal advice on whether such a clause is enforceable and whether it affects her tax position.
She should also confirm from the official terms who holds the application under corporate sponsorship and what happens to it if the employment ends mid-process. Treating the arrangement as a loan, a bonus or a gift has different consequences, and those should be settled with tax and employment advisers rather than assumed.