To change a 512/512 KB machine to 1 MB chip you need
- 1 MB Agnus
- change the A19 jumper to map the 2nd 512 KB to $080000 (instead of $C00000)
- cut the _EXRAM trace or jumper to disable the $C00000 RAM
The 1 MB Agnus by itself doesn't cause any incompatibility issues.
Some (extremely few) programs get confused by 1 MB chip RAM. For those you can add a switch to the A19 line (JP2 jumper) to switch between both jumper positions. $C00000 pseudo fast RAM will only be present if _EXRAM is active (usually closed by the trapdoor board), so you need a 2nd switch or a dual contact one.
Just don't set Agnus A19 to CPU A19 and activate _EXRAM at the same time - the machine will crash on boot-up. Also note that if you switch the A19 line while powered up the system will crash violently.