Sure, standard re-amping techniques will deal with this. However, I challenge you to play in the way you want while just hearing the clean guitar tone that is being recorded and not hearing the effect from the pedal. What I would do is record both clean (DI) and effected signals as two tracks, and then see at mixdown whether you need to re-amp to replace the effected track as the final take, or even blend in a re-amped track with the original effected track and/or the clean track.

Two alternatives.

One, use something like the MW1 Studio Tool I think it is called. This is basically a rackmounted DI/reverse DI box which allows insertion of studio-level gear into guitar chains, or stompboxes into mixdown chains. As Boswell says, you will lose dynamics, this is more I think for if somebody gives you a mix and they made a mess of the guitar sounds, its a rescue tool.

What I do is again what Boswell says but from a guitarist's point of view; delays and time modulation effects interfere with speaker excursion.

Therefore if I have time-delay effects going (chorus, flanging, pitch shifting (the worst culprit), delay etc) I run a 100% dry signal back to my main cabinet, which is just behind me (for live use). I then have another 1x12 cabinet where I run the 100% wet signal so on-stage and out front, it sounds normal, but for recording and phase purposes, the signals are split and decoupled.

You obviously, or ideally, need two guitar amps for this, I use a Rivera S-120 stereo amp, but in fact, the echo/effect sound is much less important and you can sideline it to virtually any amp. The benefit gained by keeping your main speaker's transients, attack and feel unaffected by any bouncing sounds is far outweighed by any slight loss of quality by using a secondary amp for what are effectively FX return channels.