Great question!
I think any theory or process taken to the extreme is bound to have negative effects, and cleaning/uncluttering is no different.
Off the top of my head:
- At one point, my dad was job hunting and had a few contacts scribbled on a scrap of paper that had somehow drifted to the dining room. My mom (who loves to throw stuff away) found it, thought it was junk and threw it out. The aftermath was not pleasant.
- I used to read appliance manuals once, then recycle them. This is not a good idea when, a couple of weeks later, you can't remember whether your oven's temperature is in Fahrenheit or Celsius (my oven can show both) or how to switch between one and the other.
- I toss old contracts, bills, statements etc as soon as I no longer need to keep them (legally and practically). Good practice; the trouble comes when you need to, for whatever reason, remember all the addresses and phone numbers you've had over the last 10 years... there were 5 of each, in my case.
Mine are not extreme examples -- then again, I'm not obsessive about cleaning or uncluttering. These incidents have had no lasting negative impact on my life (all the info was retrieved eventually), but they were a momentary drain on our time, energy and nerves -- which is what uncluttering is supposed to save. So yes, I can definitely see how taking uncluttering to the extreme, or even a bit too far out of your comfort zone, can defeat its purpose and become a negative rather than a positive.