Hi friends.
In a project, I imported a midi file (which was made with my Yamaha keyboard). Then I inserted a soft synth VST to some tracks, and also recorded some audio tracks from keyboard. 
Now I mute some tracks which I don't need, and make solo other tracks (midi and audio and synth tracks), and select Tracks > bounce to tracks, and select entire mixing, but some midi tracks don't exist in final track. 
For example there is a trumpet, piano, bass guitar, string (midi VST), and drum, Brass, Clean Guitar (audio), but after bouncing to one track (or even after exporting) I can't here bass guitar and trumpet. 
WHY?

Try Archiving the tracks you do not want and then hiding them.  Then select all and do the bounce see if that works.
 
I suggest this as it sound very much like something is getting muted that you are not intending.

Is it possible the missing audio is coming from MIDI tracks routed to Microsoft GS Wavetable synth? If so, you may want to disable the device in preferences and add instances of TTS-1 to the project to play the missing sounds.

An alternative to bouncing is File > Export > Audio
 
Under Source Category, choose Main Outputs
 
The other options (Channel Format, Sample Rate, Bit Depth & Dithering) will depend on where you want to listen to your mix.
Ensure everything in the Mix Enables section is checked. If you select fast bounce you cannot also select Audbile Bounce or Live Input