its very likely the internal battery that holds settings is dead.

that would be the first place I look.

And I'm not talking about the big battery pack, this one will be internal to the chassis, and is LIKELY to look like a couple shrink wrapped coin cells. (maybe one)

There are three bateries. The main battery which works for half a minute, the cmos battery which I replaced and works. And a 3 cell NiCd battery which is dead and therefore disconnected. But this battery is to hold charge and system running if you want to change the main battery and the whole time is under voltage from main source. Therefore I do not think that this battery is needed to work properly.

So some news about my problem.
I met really great people, who helped me very much. Definitely many thanks to those people, because they teach me also many things.
Now is possible to switch the frequency over debug, without restart of machine. It is not the final solution, I plan to make some sort of driver, but I have to learn many things first.
But it will be still great to have it working as it was working in the past, so if still someone owns this machine and is the speed switch by him fully working, than please send a message.
Here the debug solution.
Switch to 16MHz:
oF073 DA
ow1072 9000
oF073 00
Switch to 8MHz:
oF073 DA
ow1072 1000
oF073 00
I made also some batch files, so if wanted there it is:
https://webshare.cz/#/file/CANezY1Lxd
standal