I'm not the one to help, I am very aware of my playing and have never come across what I think you are referring to, this extreme. Good mics and technique sure help. Is he hitting wood that's creating that low mid 400/600 hz or there-abouts ? It would be good to hear an example ya know. Could you let us hear what it sounds like?

If it sounds good acoustically to you, you can be helped.
What Mics are you using, your gear profile and room? This is where your issue is.

This is going on right now. http://recording.org/pro-audio-gear/44950-mic-acoustic-guitar.html#post345777

I have encountered this more than once. It is the guitarist hitting the guitar with such force as to drown out the string sound for that moment in the beat. Just like actually hitting the top instead of the strings. The only cure is to get him to change his attack for the recording purposes.

In a solo situation this can be dynamic to the sound. Richie Havens always did this in his playing. Of course he wore holes in the tops of his guitars.

A dynamic up close will tame this somewhat and a room mic with proper placement will get you the sound of the instrument in a space. The space could be a friend or a foe depending on the acoustics.

Try to get the player to cooperate for the recording. He should be able to get the same rhythmic effect without blowing out the mic settings.

Hi KB, I have fixed string noise issues with multi-band compression before. It's not my favourite approach but if it's a good take (musically) that you'd prefer not to have to re-record, it's worth a shot as it can help salvage the track.

I will typically only use one band of the multi-band compressor (a good software-based one is fine - I use Sonitus Multi-band compressor which can be found in Cakewalk Sonar) to fix problems like this. For example if the majority of the energy in the string noises are in the 4KHz to 8KHz region, I'll setup a band to cover that span of frequencies, and bypass all the other bands on the compressor (the thought being that we only want to zero in on, and deal with the offending issue). Please note - this step requires careful listening and even the help of a specrograph to be sure you're locking in on the right range of frequencies (although this process gets a lot easier with practice and experience!)

Next, I treat that band as a limiter (I'm not looking to raise the volume of that band at all, I'm just looking to limit those peaks on 2&4). If the guitarist sounds great except on the 2&4, then you'll see the peaks in that band on 2&4 (as long as you have selected the right frequency range), so you can now setup that band to limit those peaks to the degree that they start to sound good to your ears (depending on how narrow the band is, you can be fairly aggressive with this if necessary - high ratios and fast attacks/release times). I will solo that band first just so that I can hear what I'm doing and when I get it the way I like it, I unsolo and give it a listen.

The result is that the majority of the performance should be untouched, just the peaks for the 2&4 chunks (in the frequency range you chose in the MB compressor), and only when they get to a certain amplitude. If you've done it right, the effect of what you've done will be barely noticable other than the fact that the problem has been fixed or at least improved to a high degree.

Depending on your mic position and the type of mic used, you may also be hearing a bass "thump" on the 2&4 (sometimes it can be even caused by wind motion depending on how close the mic is to the guitar player's hand etc). Sometimes the solution is as simple as a low shelf at 80-120Hz, but sometimes, Multi-band comes in handy there too if you want to preserve the bass component of the performance. You can apply the same principles as above - generally I find if the thumps etc are that offensive then they are significantly louder than the rest of the recorded material (that is, they are easy to zero in on and fix with multi-band compression).

Again - this isn't my favourite approach but it has definitely worked for me! Best of luck with this.
R

If you can't teach the guitar player to stop murdering his guitar I suggest you look for something like ReNovator from Algorithmix .
You can easily get rid of almost any unwanted sound in your mix or track, like a motorcycle in an open air concert, a shout or a dropped bunch of keys in a classic concert.
It is close to witchcraft.. ;-) ... The rest of the signal or music stays untouched... For example, with the demo I filtered the snare out of a song from CD...
Wavelab has a similar function from the same developer, just not as powerful.