leave it in. it can only be benficial. a filter cartridge is just floss and carbon in a package designed to fit in the HOB or Eclipse filter. I say leave it be. im running a 5gal nano REEF and its doing fine with the HOB filter in place. This being said...
You say your tank is cycling, the carbon in your filter is going to remove alot of whats needed for your nitrogen cycle. If you have the filter in place and your tank has already started to cycle, leave it be. if its been a while and your tank is JUST NOW starting to cycle, pull it and replace it (with a new one) after you have cycled...
Hope this helped