Normally designation of key employee status must be made at the time the leave begins, or when the employer is made aware of the need for leave, whichever is earlier. The employer must show that you qualify for key employee status, and that your reinstatement would cause it "substantial and grievous" economic injury in order to deny reinstatement. The fact that they are using the key employee provision to deny reinstatement coupled with their actions questionning the medical documentation raises suspicions that they may be violating the FMLA.
I suggest you speak with an employment attorney as these cases are very fact specific.
Also, you can review the Federal Department of Labor website regulations at 825.217-219 that will shed greater light on the subject.
Licensed in CT and FL
The fact pattern you provide does lead one to question whether the employer's actions might constitute "interference" under the FMLA. I don't see any "retaliation" claim yet since there has been no adverse employment action against you. Recertification requests are proper but the timing of them is governed by DOL regulations as noted by the other attorney and by the Code of Federal Regulations interpreting the FMLA. The same is true for designation of "key employee" status. You should definitely speak with a local attorney who is familiar with FMLA matters so that you can go through a more detailed question and answer consultation.