Audio/MIDI/Tempo problem

[Galapas]

I run a small home studio and record demos and CDs for local bands and I regularly do drum replacement on my multitrack audio. I usually MIDI map the entire song manually by referencing the drum track(s) and using the "Set measure/beat at now" feature at quarter note intervals giving a good representation of the tempo of the live recording. This allows me to [manually] input the MIDI notes to coincide with the audio drum parts. Yes, I know there are "automated" ways to do this, but I have my own reasons for doing it manually.

Occasionally, in inputting the MIDI notes, I find a tempo marking that was marked wrong or missed. That's where my problem starts.

I know that after the MIDI has been input, that changing the tempo map can affect the position of the MIDI notes (sometimes leading to disaster as you will see),  so I'm cautious of doing this at all. If it happens, I usually "Cut" my MIDI to the clipboard (without copying tempo) and make the tempo changes, then paste the MIDI back in, in which it will now follow the new tempo map. If I don't "remove" the MIDI, this is when the disaster occurs.

My recent example:

I was mapping a rather long, complex song using the method described above and as I was reaching the end of the song while inputting the final measures of MIDI notes, I noticed a tempo mark that was out of place which would throw the remaining MIDI off beat. Having been working on this song for a few days (MIDI mapping, setting up the drum sounds, inputting MIDI, etc), I was eager to finish as I was on the last 4 or 5 measures or some 100+ measures of complex drum parts. I figured since I hadn't input any MIDI notes PAST the bad tempo mark, that it would be safe to change the tempo mark without cutting the MIDI first. I first deleted all tempo marks from the bad mark until the end (about 4 or 5 measures), then remarked the tempo (per quarter note) to the remainder of the song. I then proceeded to finish the MIDI input out to the end of the song.

I then did a playback check to see how it all sounded when I discovered that the last actions had caused the original MIDI notes (before the tempo change) to be copied into several clips (19 clips), in layers from random parts of the song which were all in the wrong locations. All of which were overlapping each other and many clips randomly jumping to later parts/measures as if they were in order (if that makes any sense). I immediately copied the entire MIDI track to another file (for safety)  and used the "undo" function to go all the way back to the point before I changed the tempo (I have "undo" set for "unlimited"). Though "most" of the rogue clips disappeared, what remained was about 4 clips (was originally one long clip) which were all in the wrong place and some were missing. Some could be expanded (length dragged) to reveal this missing parts, but again, everything was wrong. In my opinion, the "undo" should have restored it to it's previous state, but actually made it worse.

It will now take hours to sort through the remaining clips to place each section where it belongs and delete any repeated sections.

This is not a new issue. It has happened many times before and is the very reason I had started "cutting" the MIDI to the clipboard before doing such tempo changes. The issue goes back as far as I can remember (long time Cakewalk user). I'm not sure if this is a bug or some simple setting I need to fix, but I just lost many hours of work in just one tempo change and no, I didn't have "auto save" or "auto backup" turned on (for personal reasons), so my only save is many edits old, but may help me save most of the file.

Does anyone have a solution or know the reason this is happening? It has "bugged" me for many years.

Thanks, Bill P.