Hi, Joe! Welcome to YamahaSynth!
We moved your post to the “Legacy Yamaha Synth” forum as a Motif ES (2003-2007) qualifies...

I have an es8 that had a yamaha breath controller bc3 installed. I have done a factory reset a couple of times. In pattern mode, sound 1 has a trombone sound that I cannot get rid of and it layers on top of whatever I assign to 1 - I have tried copying blank patterns and it still remains - I rather suspect this is all related to the yamaha breath controller bc3 but I cannot find any info on how to de-install it -

A BC3 is not “installed” so we are not sure what you are talking about, exactly.

A BC3 is a controller, see one here: Yamaha BC3 (Discontinued).
Like a Sustain pedal, you plug it into the dedicated jack — this is not “installing”, it is simply connecting.

Perhaps you are trying to indicate you have a PLG150-series Plug-in Board that you don’t know how to use.
We are just going to assume that you have a PLG150 board plugged into slot 1 of your instrument. (The Motif ES had three PLG slots). If we are incorrect, just ignore the rest of this....
PLG150-AN, PLG150-AP, PLG150-DX, PLG150-VL, PLG150-DR/PLG150-PC, PLG150-PF — each is a separate synth tone engine on a plug-in Board. Each can stand alone and contribute a synthesized sound...

If you don’t want the PLG150-series board to sound along with the internal sound you place in Part 1, you can change the Port and MIDI Receive Channel of the PLG150 Board to something different from the internal sound in Part 1. Of course, if you place it on the same Port and MIDI Channel, it will layer with the internal sound in that Part.

A “Port” is the equivalent of a MIDI IN and MIDI OUT — 16 channels in each direction.
A “Channel” is a discreet communication bus... there are 16 channels going and coming.
The internal Motif ES occupies Port 1

The internal Motif ES sounds in Parts 1-16 of a Song/Pattern Mixing all are fixed on Port 1, and each can occupy a Channel, 1-16
If you want to keep your PLG150- series boards separate, place them on Port 2, and select a channel between 1 - 16 for each Board so it has its own discreet receive channel.

Press [UTILITY]
Press [F6] PLUG
Press [SF1] STATUS — Here your instrument will report which PLG150 boards you have installed and in which slot they are located, 1-3
Press [SF2] MIDI — “Device Number” should be used when you have more than one board of a particular type you can differentiate between them when sending MIDI messages with the ‘Device Number’... otherwise leave this set to “all”
“Port Number” — Determines the MIDI Port number over which the Plug-in board receives MIDI data in the multi-timbral tone generator mode (Song/Pattern modes).
___ Set your PLG150 Series Board to Port 2.
This will allow it to have its own Channel and will stop it from playing Part 1, Port 1, Channel 1 which as you know, is an internal sound.

See page 265 of your Owner’s Manual for additional details