Agreed, there is always a chance. Assuming you're using a wine thief (or something similar; turkey baster?) and are careful about using it properly, you'll be fine. Not sure about your methods, but I know some people add the tested sample back to the batch...I wouldn't, especially in this case.
Cheers
You will be fine taking samples. The time that the beer is actually exposed to air is relatively short. It's common practice to routinely take samples to check FG readings and ensure fermentation is complete. Just don't ever add the sample back to the beer. This can cause an infection and isn't worth the relatively small amount taken in a sample. I'd say take the sample and try it afterwards. RDWHAHB. Cheers.