If yours is not an aftermarket top, I doubt that it is fiberglass. What I’ve seen on factory tops seems to be a double wall formed plastic. If it is fiberglass, use care not to sand through the gelcoat.
I painted a halftop 10 years ago and it is still holding up well.
Since the repaint on yours is flaking, you need to remove all of it.
I would suggest NOT removing the factory paint, assuming it is not flaking. It will serve as a good base for your new paint to stick to. If you do remove the original factory paint, you may want to look into an adhesion promoter.
A good paint job required good preparation. My halftop was in factory paint. I sanded with an electric sander and some spots by hand just enough to scuff the old paint well. After the sanding, all the dust needs to be removed with a tack cloth.
If you are mixing your own paint, you may need to add a flex agent. I painted mine with rattle can Rustoleum. I think I used 3 coats to cover the black with a spice color, alternating the spray pattern 90 degrees on each coat.
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