Upvote:2
The advice you received is a bit surprising. It's true that you cannot get a Schengen visa that would overlap with another valid Schengen visa but it seems strange that a visa that has already been used would count as a valid visa. In any case, it should be possible for the Maltese consulate to invalidate their own visa and replace it with another one if they want. The only thing that they cannot do under any circumstance is grant you another uniform Schengen visa if you have already stayed more than 90 days in the area in the last 180 days.
Now, if you visa mentions 45 days under βduration of stayβ, then you are still allowed to stay another 45 days before hitting the 90 days limit but not with this visa. So if you used up your 45 days, you definitely need another visa to reenter the Schengen area. In any case, the advice about staying 45 days outside of the Schengen area makes no sense to me. Did you perhaps stay in the Schengen area on another visa before February?
In any case, if you already used up the duration of stay mentioned on your visa, I don't think it's safe to travel.