x2 on what racekid said. Although if your talking about dropping the pan and changing the filter it probably wont be a problem. If your totaly flushing the entire transmisson you may notice problems and it can also cause your transmission to shift hard and slip a little. This is because the abrasive material that wears off the clutch packs helps to work as a friction material and without it in the fluid your transmission may slip for awhile. If you do flush it you should put an aditive in it to help it stop slipping. I know that lucas makes a decent one and I think Bars also does. I know the lucas one works pretty decent because I have people come in to work a lot explaning how they flushed there system and then it slipped. I recomend they use the lucas stuff and they said that it has helped a lot.
Also check your wheel bearings, balls joints, tie-rod ends, shock absorbers, ect...
Also check your wheel bearings, balls joints, tie-rod ends, shock absorbers, ect...