As an example
「明日、行けなくなっちゃうよ？」(talking about a date etc.)
How can you tell here whether it is 行く negative potential form or イケる negative form? As far as I can see both look like they'd make sense. イケる still works written with kanji so I don't know how to tell them apart.
Do you mean this by イケる? Then this is etymologically the potential form of 行く. Simply, something like "go-able" became a fixed phrase meaning "(will) be fine". This イケる is a derivative fixed expression that is usually used in the non-negative form. We say イケるよ ("It's gonna be fine"), but we rarely say イケないよ ("It's not gonna be fine"). For the latter sense, we normally say ダメだよ (or いかんよ, although this sounds pompous) instead.
Therefore, 行けなく in 行けなくなっちゃうよ almost certainly is the negative potential form of 行く, i.e., "not to be able to go".
明日、行けなくなっちゃうよ？
You won't be able to go tomorrow, you know?
