Trying to the zip after collecting the all the spores in the sewers but I lose the storage after the cutscene where Batman turns around and aims a batarang, I've tried using another gadget like the twin batarangs but I still lose it. I've also noticed (in the video) that he pulls out a normal batarang during the cutscene but he still keeps the storage. I've done that accidentally before and equipped the explosive gel before the cutscene plays but I still lost the storage. Quite baffled thus far

Storage shouldn't have anything to do with that cutscene. Make a video demonstrating the issue, I find it hard to believe that you aren't just equipping the batarang by accident, or somehow not actually getting storage in the first place.

Tried to make a video using the two ways of equipping the gel and the twin batarangs before the cutscene but they recorded at the wrong fps and so it looks like a slideshow. I did keep the storage for the first attempt though (Equipping the twin batarangs). The second one I lost it (equipping the gel) but I think on the second run I equipped the batarang without holding the left trigger which I tested and only just found out that you lose the storage from that. Idk how I didn't know that but I think it's safe to assume that's I was doing wrong. Cheers though.