I found a solution which may help anyone else who has a similar problem.
Because I had already upgraded to windows 10 before performing the factory reset I was able to create a windows 10 boot USB stick and install a fresh copy. This effectively bypassed the acer boot partition which is effectively now redundant.
If you want to create a windows 10 boot usb follow this link https://www.microsoft.com/en-gb/software-download/windows10 then click on the 'download tool now' button and then follow the instuctions. You will need a USB stick of at least 4GB (8 would be better) and it will wipe all the files from your usb stick.