a lot of shrimp are pretty sensitive and will die if you don't remove them. make sure to remove most of the current water and thoroughly wash the flourite, then fill slowly to minimize the flourite cloud. put in a corner filter, or stuff the current filter with filter floss b/c it will also help to clean up the flourite cloud quicker.
what size is your tank, what filter do you have, and what plants are you growing?
I've got a 20 gallon with a fuval 104 on the side. As for plants, a tad of dying HC, some HM and everything else is pretty simple to keep. So adding Flourite is going to cause an ammonia spike? I thought that was for the Amazonia stuff..?
no ammonia spike, the flourite will make the water cloudy if you don't wash it thoroughly. and shrimp will get stressed out too much and die. besides, since i think you are going to uproot the plants and replant them after adding flourite, you should do a water change afterwards and make sure to remove the shrimp beforehand.
the filter floss is just to help with sucking out the flourite dust cloud.
You can always get an ammonia spike/minicycle when disturbing substrate. Keep in mind that N-bacteria are aerobic, and if any end up buried deep enough that their O2 supply is restricted, they will die off. Just a warning to keep an eye on your tank parameters for a few days; a water changes should keep things up and running.
Personally, I'd remove the shrimp to make sure they don't get buried.