OP, you should consider consulting with an employment law attorney first to better insure your interests are protected.

Following a consultation with knowledgeable counsel, you will have a far better appreciation for what your rights are and how to proceed. For instance, it was likely improper for your employer to count three weeks of cumulative work time as FMLA leave. In addition, if your employer retaliates against you for exercising your right to take FMLA leave, you would likely have legal recourse for challenging such adverse employment actions.

In contrast, HR works for the company. While the employees in your company’s HR may be honorable individuals, they do not work for you. Similarly, DOL staffers will not necessarily advocate on your behalf.

After consulting with counsel, he or she will probably recommend you apprise HR that your supervisor compelled you to work three weeks when you were on FMLA leave. (If for no other reason than to preserve your remaining potential FMLA leave for this twelve month period, you likely should tell HR you actually had to work the weeks in question.) If necessary, counsel may even direct you to file a complaint with DOL.

Before taking any steps, though, you want to know the legal and practical ramifications of your actions. A consultation with private counsel can provide you with such a “lay of the land.”