Fury and the rest of the World Security Council were kept successfully in the dark about Project Insight's true nature until the last one or two days before launch. The "cover story" would have been believed as fact by a wider range of SHIELD personnel, probably including Fitz.
Not sure what that means in relation to how many non-Insight 'Carriers there were/are and what their situations are...
Being someone who has a degree in Computer Science and have done years of university research in AI at postgrad levels, Project Insight looks like something that is implemented as a piece of AI software.
Which means no hardware changes are required on any of the Helicarriers. Project Insight is just requires a simple software update. This is supported by the fact that all Cap needed to do was swap out a tiny module in the carrier's data core.
If all the above is true, it makes sense for Hydra to install Project Insight on every single Helicarrier. So it is likely that the old helicarrier has been scrapped and the 3 new helicarriers we saw are the only helicarriers Shield currently owns.