A couple of years ago I got a friend into GTD. He was already an experienced Vipassana meditator, while I had only recently set out on that path.
The first question he asked me was this:
GTD recommends that you capture everything as it occurs to you. How do you handle that when you're sitting?
I've never experienced conflict between GTD and meditation. Perhaps because I got into both at about the same time -- within a year of each other, though it's hard to calculate what with falling off the wagon all the time.
Like other keystone habits, both practices have ripple effects that impact one another in a positive way, even if they seem at odds.
Here's how I replied to my friend at the time:
I have an agreement with myself. If a thought occurs to me during meditation that I think is important, I break the sitting to capture it.
But if I decide not to capture it, I let it go. I don't try to hold on to the thought at all.
That's the trap: committing to neither practice, wavering between them.
Of course, thoughts don't pass away just because they're inexpedient. But the agreement reminds me that if this thought was really important I would have captured it already.
Another way of thinking about it is this: What would you do if you were trying to get out of the rain when the thought occured to you?
Would you stop in the pouring rain to record the idea, getting drenched in the process? Or would you wait until you reached shelter to record it -- at the risk of having forgotten it?
Since I gave this reply, I've fallen off of a caravan of wagons. But honoring this agreement has been good to me, as I keep on re-discovering that almost nothing is important.
In these two years I have broken my sitting maybe two or three times to capture a thought. I have stopped in the middle of a rainstorm to record something only once.
The rest arises and passes away as it wills. Forgetting to buy some groceries or to call someone back is not a big deal. Being reactive to your own internal input is as pernicious as being reactive to every email or text that lands in your inbox.
Give yourself permission to sit quietly, and to not get things done.