My employer has sent a letter stating my Fmla has ended, then asked for documents affirming my intent to return? Also, asked for medical progress.

FMLA protects your return to work rights for up to 12 weeks.  If you are going to miss work beyond that period of time, the Employer can ask for medical proof.  The Employer does not have to rely upon the MCO and can ask you directly.  Your failure to comply -- depending upon the existence of writte work rules -- can result in your employment being terminated which could then impact your right to receive temporary total disability compensation. Note that once FMLA expires, your Employer can legally fill your position leaving you with no job to which you can return, effectively terminationg you.  If there is a union collective bargaining agreement in place, this result may be altered. As for the PTO, again you need to look at whether there are any written work rules that address PTO scheduling folowing FMLA.  As longa s the employer is applying the same rule across the board, then a discrimination claim is difficult to prove.