I had the same problems working on my dissertation when there were just so many citations. I tried a few things to get it to stop and finally did, but can’t remember how I did it for sure. On the General tab of the Endnote CWYW Preferences window (found in the Word - - Tools - - EndNote menu) there is a box for “Enable instant formatting on new Word documents.” I have that turned off now, so that might be it, but I don’t think so. The next line below that box to "Turn off Word’s “Show Field codes instead of their values” also might be it, but that doesn’t ring a bell, either.
I believe the correct command you want to use is under the Word–Tools–Endnote menu, then select “Bibliography Settings.” On the “Instant Formatting” tab of this window, you want to turn instant formatting off by hitting the Turn Off button. This prevents your paper from updating every citation every time you enter a new one or rechecking every citation every time you add a new one or every 90 seconds (the default).
Those are the only things I can think of. You might be better off looking for a thread that matches your question better, though, or starting a new one. This thread is not anywhere related to this topic, so nobody else might even think to respond to it here.
Dave