No, it will not harm your transmission when done correctly and or on time as long as the manufacture (Lexus) doesn’t say other wise… Flushing a transmission will get almost all the ATF exchanged, including the torque converter and moat all the clutch packs etc etc normally… If Lexus says it is OK to flush, then flush it, check your owners manual to see if/what it says… We are not talking about if the dealer says it’s time to service the transmission or not, only that it is OK to flush or not…
What people are scared and talking about damaging the transmission is when it has never been serviced and then you want to service it at high milage and or you start having trans issues…
I wrote this a while back and it is about automatic transmissions in general…
Changing your fluid cannot cause any damage by itself, if everything is fine inside the transmission… The issues start to appear when you change the fluid if your clutches are already worn or damaged from use. If you go and replace the fluid after they are already worn out. this can cause slipping…
For more info and pictures, click on link and read away…
Also:
Transmission Flush vs Fluid Change: Which is Better? : AMSOIL.