Yes, of course, fragrance can make you sick! Smelling ONE candle is one thing. Inhaling chemical fumes from 250 candles (or the wax blend to make them) is quite another.
With this much production and (I'm guessing) no control over the amount of fragrance chemicals in the air, it's a small wonder you're not feeling well.
I highly recommend that you increase your overall building ventilation considerably with a large input of fresh air. If you're doing this work in your home, this addition of fresh air is even more critical -- you're spending up to 24 hours a day exposed to these fumes, not just 8 on-the-job hours, so getting rid of the vapors in the air is vital.
Next, look at a ventilation hood to be used whenever you are handling the fragrances. Using a hood will remove vapors at their source.
And finally, wear an organic vapor respirator as much as possible while you're working with the fragrance. A respirator is good for personal protection for short-term protection. It's no substitute for controlling the overall air quality in your work space (and home).
Another thing is fragrance chemicals may be absorbed through the skin and mucous membranes, so chemical resistant gloves and goggles are also wise.