An employee cannot be treated differently or have reduced benefits due to the employee being on FMLA leave or because the employee has a disability. All employees must be treated equally. However, an employer does not have to put an employee back to work if they took more than 12 weeks of FMLA leave or if they cannot do the essential functions of their job. You need to consult with an attorney to provide more details to get full legal advice.
This is not intended to be legal advice, but is only for general information. Cantact an attorney in your area for legal advice.
There are a lot of potential FMLA and ADA legal issues in your situation. There are too few details here to adequately address your question. You need to talk to a local employment lawyer about this situation.
Is this "freeze" company policy or just for this employee. The company must treat all similarly situated employees reasonably equally. As was stated above, you need to contact an attorney to discuss these serious health issues.