The "replace existing trades" checkbox next to each importer should be checked when you are importing data from the same exchange multiple times within a tax year. Checking this box will ensure that duplicate data is not imported.
For example:
I imported my 2020 Binance CSV in Feb 2020 - it contained my trades from Jan 2020 through Feb 2020. I then did more trading on Binance and at the end of April 2020 I wanted to add those new Binance trades to my 2020 tax year. I can import a newly exported Binance file, which contains all of my trades from Jan through April, and as long as I check the "replace existing trades box", only my NEW trades from March and April will be imported; the trades that I already imported, from Jan and Feb, will be ignored.
The replace existing trades checkbox only affects the specific exchange you are checking the box for and only affects data for the tax year you are working within.