Find/Replace Regular Expression limit

Please don't mix REG_REPLACE() from e.g. SnowFlake. PSPad doesn't use such function and such syntax. It doesn't mean when one programming language contains such function, that it's general function over the whole world.

The error is in the RE (.*)(b|c)(.*), not in PSPad.
The first term (.*) matches the longest part of "a b b c c b b d" until one b or c is left. So the result "a b b c c b ~ d" is correct.

A solution to your problem is:
Find: [bc]
Replace: ~

The same logic applies to the SQL problem. Don't make things more complicated then they are...