It should be ok in a few days, just remember that any fast changes in your water parameters can be just as harmful imo as when you get a contamination enter the system. If you have access to another hob filter system you could set that up as well for a few days if you have room in tank or sump area. The filters and carbon are the big key to clearing up your water and will eliminate odours as well. The water changes will also help.
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