I don't see anything wrong with being honest in this situation. You aren't being rude or saying you have a problem with her - you just can't tolerate strong fragrance.
Say it conversationally and it will probably be easier. Make a comment about how you hate that you can't tolerate most fragrances, because there are so many you like. Tell her you really like what she has on (okay, so maybe a little white lie might be needed here, haha) but that for some reason it keeps making you sneeze. And then ask if she wouldn't mind not wearing it to the office, politely.
The other option is to be all dramatic, say you have a horrible headache, say someone must be wearing some really strong perfume because that's what usually triggers them for you - and hope she gets the hint.
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