The simplest answer for this problem is to use dyadic >. (Larger of) ...
0 >. y2
0 0 0
1 2 3
If you want to use a more general conditional replacement criteria, then the following form may be useful:
(0 > y2)} y2 ,: 0
0 0 0
1 2 3
If you want it as a verb then you can use the gerund form (v1`v2)} y ↔ (v1 y)} (v2 y) :
(0 > ])`(0 ,:~ ])} y2
0 0 0
1 2 3
If your question is more about scatter index replacement then that is possible too. You need to get the 2D indices of positions you want to replace, for example:
4 $. $. 0 > y2
0 0
0 1
0 2
Now box those indices and use dyadic }:
0 (<"1 (4 $. $. 0 > y2)) } y2
0 0 0
1 2 3
Again you can turn this into a verb using a gerund left argument to dyadic } (x (v0`v1`v2)} y ↔ (x v0 y) (x v1 y)} (x v2 y)) like this:
0 [`([: (<"1) 4 $. [: $. 0 > ])`]} y2
0 0 0
1 2 3
Or
100 101 102 [`([: (<"1) 4 $. [: $. 0 > ])`]} y2
100 101 102
1 2 3
To tidy this up a bit you could define getIdx as separate verb...
getIdx=: 4 $. $.
0 [`([: <"1@getIdx 0 > ])`]} y2
0 0 0
1 2 3