Unwanted patch change in the midi clip

Any time you delete a synth from the synth rack that has tracks associated with it, you are inviting a mess.
It's just bad mojo.

I personally do not like "Simple Instrument Tracks". They are intended to be "simple", but if you try to do anything moderately sophisticated, you are severely restricted. I think they were developed because so many new users were confused by the relationship between the MIDI source track and the synth audio output track.
The downside is that, while  a simple instrument track works, it does not promote understanding what you are working with.
Case in point.
Yes, you are limited in the number of synths you can insert in a project. I believe MC is limited to 8(could be wrong on that).
With simple instrument tracks, you are going to hit the ceiling really fast.
However, if you use a synth like TTS-1 to its fullest, you can have 16 MIDI tracks feeding one instance of the synth, and have 4 audio outputs. This is not possible with simple instrument tracks, but is very easy with separate MIDI and audio tracks.
That is my preferred method, because you have much more flexibility and control.

I started out years ago trying to do this right, by buying the right tools.....software DAW, interface, monitors, computer.....then I started to grab lots of "free" VST's and synths from the net. 

Pretty soon I had a sizable collection of mostly mediocre stuff. Really not much better than the TTS general midi stuff.  While TTS is an amazing synth and is capable of running 16 tracks with 16 different patches at a time, the sound quality, unfortunately is on the lower side of the bell curve. (for my needs and concerns)

I have heard some really amazing things from people who take the time and work with TTS to create a masterpiece. 

So, when I finally decided to build a DAW and move from the laptop to a custom machine, I also had a serious look at the synths and FX I was actually using, and I migrated only those VST's to the new system. 

Somewhere along the line I decided to buy the Native Instruments Komplete package of synths and BiaB.... not cheap but definitely some high quality and good sounding stuff....it came to the new machine, and I had purchased a few other fairly nice tools, and they too were migrated over. Included in that are Melodyne, and Ozone. Both are FX. I occasionally use some other things but these are the main ones. 

All of the free stuff stayed on the lappy since it fell into the category of rarely if ever used. I do not miss using the SFZ and TTS patches and sound fonts. 

Now, I have a small selection of synths and FX that I use. These tools are used on just about every song I work on. These  things are the mainstay and the foundation for every project I work on. With them, I can do everything I need to do, and everything on my songs page is created and recorded with them.....and with a few live instruments that I play, such as the occasional piano part, guitar parts and mandolin parts.... plus vocals.