Avoiding clipping from external distortion effect

[unfunfionn]

I decided to start playing around with the External Audio Effect and some distortion pedals I had for bass guitar today, and the results are actually really nice apart from the awful clipping I'm getting unless I gate out the higher frequencies completely, which I don't necessarily always want. But with the clipping, everything is sounding a bit Raster Noton.

What can I do to prevent this? Is it simply a case of limiting the input signals, or is there a straightforward way of removing the clipping from clips I've already recorded?

What I did:

Acid Meltdown preset > External Audio Effect > Scarlett 2i2 audio interface (output 1) > Electro Harmonix Bass Big Muff > Scarlett 2i2 line input 1 > Recorded to additional audio track

Sorry if this is ridiculously newbie.

Thanks!