Jlien X
When I'm in the songwriting stage, note events of almost all MIDI clips are 100% quantized for convenience. After I'm happy with the chords and melodies, I randomize (humanize) all note events on all non-keyboard instrument tracks (e.g. drums, brass, strings). As for keyboard instrument tracks (organ, piano, etc.), I want to play and record the take myself without quantizing because I practice keyboard 
So, I need to delete just musical data.

Cool :)
I'm mainly a pianist/keyboardist myself. I can't recall any organ/piano patches I've used that have key switches though, so in these cases I've had no problems just deleting the whole cips and re-record.
 
When it comes to patches with key switches I don't think I have a standard method. It depends on various things if I choose to record or if I just open the PRV and draw the performance. I've always been a MIDI-drawing-nerd. I think this developed when latency always was an issue and you had to draw to get the notes where you wanted them. Today I "read" the PRV as easy as any sheet music and can draw any kind of performance with no trouble at all and hear the result in my head long before I play it.
 
If I just need a simple chord structure with a patch that have lots of key switches I usually record the chord structure live and then edit the details after. The more complicated the performance the bigger chance of just opening the PRV and drawing the whole thing from scratch.
 
Especially if it's an acoustic instrument (like guitar, brass, viloin ect) I can sit for hours in PRV nudging notes around and fine tuning controller data just to get exactly the feel I want. I never use randomized quantizing though. I want full control of everything. It's important for me that even the "timing errors" in a performance "feel right". Yes! I'm a control freak when it comes to music. It's time consuming but IMHO it's totally worth it! :P

Loptec

I'm mainly a pianist/keyboardist myself. I can't recall any organ/piano patches I've used that have key switches though

Hammond B3 and C3 organs had keyswitches, the lower octave with reversed colours on each manual consists of keyswitches for different drawbar settings. (maybe the first implementation of keyswitches?).  Native Instruments Vintage Organs and the earlier B4 II and GSI's VB3 all emulate this feature.
 
While I manage reasonably well with the options in Sonar at the moment for key switches but any improvement would be most welcome.
 
My biggest beef with keyswitches is most, if not all synth type controller keyboard options stop at 61 notes, which is too short for most keyswitched VSTis, I use a Kawai LP25 mini keyboard in conjunction with my 61 note boards and map the keyswitches to that.
 

Loptec

Jlien X
When I'm in the songwriting stage, note events of almost all MIDI clips are 100% quantized for convenience. After I'm happy with the chords and melodies, I randomize (humanize) all note events on all non-keyboard instrument tracks (e.g. drums, brass, strings). As for keyboard instrument tracks (organ, piano, etc.), I want to play and record the take myself without quantizing because I practice keyboard 
So, I need to delete just musical data.

Cool :)
I'm mainly a pianist/keyboardist myself. I can't recall any organ/piano patches I've used that have key switches though

Me neither lol (...but Glyn taught us what we didn't know, thanks Glyn). Hmm....maybe they were choir clips with key switches and I just wanted to replace the chords with better ones and mistakenly deleted the key switches with the clips....don't remember anymore.
 
I now want to give your request a big +1 because if PRV can have a diatonic key layout with key switches, I can still use a separate lane (yes, the controversial Take Lanes!) for only key switches, and note events and key switches will both appear in PRV. But the diatonic key layout must be able to hide ghost keys so that we won't have to scroll down the PRV to display key switches.

For instruments with key switches, I use custom note names in PRV, and for the notes that aren't key switches, I simply use a layout resembling the diatonic scheme:
 

C3
B2
===
A2
===
G2
===
F2
E2
===
D2
===
C2