Is it a good idea to completely flush transmission oil?

I have a Corolla, year 2000 with 5gear manual transmission and the third gear has been hard to hit recently especially from 4. I heard from a mechanic that changing the transmission fluid completely may not be a good idea since the brand new fluid would send all the debris all over the transmission causing more trouble than it would solve. What do you think? He recommends only filling the fluid to a proper level and not drainig it completely… The car has 90k miles in it.

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