A ha and ga question

Can someone help me with this problem?

So は indicates comparison right? If I say

まいこは歌が上手 - this means you are good at singing.
まいこは歌は上手 - this sounds bad because it says this is good but something else is bad.

フルーツがある - there are fruits
フルーツはある - there are fruits (compared to something else)

So this makes sense. BUT...

If i want to ask my boss if there is a reply yet I should say;
返事はありましたか？　（返事はあった？）
Why is this not 返事が? It is not as if I am asking if the reply came in comparison to nothing else coming.)

So は indicates comparison right?

Sometimes; sometimes not.

If i want to ask my boss if there is a reply yet I should say;
返事はありましたか？　（返事はあった？）
Why is this not 返事が? It is not as if I am asking if the reply came in comparison to nothing else coming.)

Well, actually you are.

返事はありましたか？
Did you get "any" replies (as opposed to none or something else)?

返事がありましたか？
So you did get a reply (as I understand you did)?

Hope it helps.