It is hard to understand your questions when you use no punctuation.
I think you are asking if its ok to run your filter. Yes, but while you are doing water changes, turn it off.
What to do with your shrimp while the mess is being cleaned up I think is another question. If you have a separate tank you could use until you replace the water, it would be a good idea to use it. Depending on the kind of soil, it could leech a lot of ammonia in the water and could kill fish/shrimp.
What plant did you add that caused you to get soil in the tank anyway?
