It’s possible the Apply changes button is disabled because the system no longer recognizes an active “AI suggestion” to apply. You can manually revise the pin order through the Inspector as described in Flux’s “Working With Symbols” documentation. Here is the relevant excerpt:

Changing Pin Order
By default, pins are sorted in the order of their pin numbers. To configure a different order:

If the “Apply changes” button remains greyed out for AI suggestions, you can instead reorder pins via the Inspector. If you still have trouble, check your Change History, or refresh your browser/project to see if new suggestions appear. You can also visit the Flux Docs or the Flux Community for further assistance.

I dont wnat to change the footprint etc for the chip, will that just change for the schematic?

Changing the schematic pin order only affects the symbol representation in the schematic and does not modify the PCB footprint. The footprint—the physical pad layout for manufacturing—remains unchanged. If you only want to adjust the schematic view, you can update the terminal order without impacting the footprint.