Your design isn't bad. I was just doing the munchkin thing.
Ok, let's go down the list of reasonable situations:
Mechanican with multiple bodies:
The only capabilities which should get changed are Nanotech and Stringtech. There's no crazy skill bonuses here and a munchkin can't get more than about 3 twists (for -12 points), and that involves tanking their best abilities. Also, the player needs to define each of the character's bodies (or burn a twist to declare that there was an additional one all along / the new body just finished fabbing / etc.). On the whole, the rules should work pretty well here.
There's no reason to peacebond Cognitech, Biotech and Metatech can't be peacebound, so the situation is the same as the Mechanican above.
Stored / Stardweller:
And now we get problems. A Stored can reasonably change their Cognitech and maybe even Metatech by changing their servers. And a Stored can change their Stringtech and Nanotech whenever they use a different remote. I'm not sure how fast a Stardweller can change their physical form, but there aren't many limitations I can think of.
When a spy lens is coupled with peace bonding, it can change everything. That said, spy lenses tend to reduce the character's professions, and change its CVs.
1) The player needs to describe what is going on and define each of the character's forms, all with GM consent (and the GM is encouraged to veto anything that looks to be abusing the system).
2) Normally Cognitech, Biotech, and Metatech are unchangeable (see above). Cognitech and Biotech represent balance considerations.
The bloody way to handle cognitech:
If your Cog was at 6 (when you get 1 year / 0.5 year) or below, subtract 1 from each Profession for each learning rate drop you take (so -1 when you go from 0.5 yr to 0.75 yr, and -1 when you go from 0.75 yr to 1 yr). This is almost exactly what the chart does anyway (except for very low skills, where this method penalizes the player a bit). When dropping from 0.25 yr to 0.5 yr, multiply all professions by 0.8 and round down. This is approximately what the chart does.
So a Cog 10 character going down to Cog 3 would drop a profession at 10 down to 6 (10*0.8 – 1 – 1).
Biotech is harder to handle since it adds actual years to a person's life, not skill. Lowering your biotech doesn't make you younger, and won't cause you to drop dead if you're already over the (new) life expectancy. For this reason, I'd recommend making biotech a bit less cost effective to decrease. Perhaps every 2 points of Bio is worth a 1 point drop elsewhere?
To be honest though, this all represents substantially more math and finagling than SA wants. And it won't stop munchkining, merely slow it down a tiny bit.
On the extreme other end of the spectrum, you can just weaken the rules:
If the player is dropping the character's capabilities by a sufficient margin (GM's discression, but lowering the capabilities to the point where the character would normally get additional import is always “a sufficient margin”), then the character is rewarded a twist (for an effective complication). If the character later brings their capabilities back up, they lose the twist, or take a complication. The GM may rule that dropping the capabilities sufficiently (or taking other disadvantages that hamper the character) may reward more than one twist, although this should only be used in extreme circumstances.
This is weak enough that if you lower your character's capabilities, you end up with a weaker character, no matter how you look at it. It does help mitigate some of the disadvantage though, making it worthwhile if it's in-character.