Can Portugal "black list" my passport because I got a visa but didn't visit Portugal with it?

To me, it looks like you initially obtained a visa from Portugal and did not travel or did not stay there and then you were going to reapply again for another visa and the embassy found out that you did not visit Portugal and now they won't issue you a visa?

Consulate office told you that they would reject and blacklist your passport; I think were more generous to you.

First they could have refused your application and second they could have stored your information in SIS (Schengen Information System) that you previously mislead Portugal and breached your visa conditions which would make your future applications more vulnerable.

I'm not certain if your question is "you did not submit your application and would they still blacklist you?"

If yes, I don't think you are in trouble

For your case best for you is go for the consulate in which you entered or exit from you last Schengen visa .That would not only make you next application stronger also it would convince the visa officer that you have entered to his country and poses no threat to further applications.

My suggestion for your next visit always stick to your plans.

I obtained Schengen visa from 15 embassies and share here one experience here:

Schengen visa for Germany: I was supposed to enter from Germany and exit through Italy, I changed my route and entered through Zurich and exited through Milan so when I again reached the consulate, I faced the similar story.

However, I still stayed in Germany and I had my paid hotel receipts along-with bus and train tickets which confirmed that I stayed in Germany.

The only problem was that I was supposed to stay in Germany for 5 nights and in the end, I just stayed there 3 nights and spend most of my time in Italy so they simply refused to accept my application.

After 2 weeks I applied from Italian consulate and they issued me the visa without any difficulty.