So bit of good news – I think I have finally sorted my Linux issue and can read memory cards again! I ended up manually uninstalling v17.2, installed a secondary hard disk in my laptop and installed v17.1 onto it. For some reason the earlier version seems to be working much better. Thankfully.
So now I will have to start from scratch again so I think I will wait for RetroPie v4 because I have read there are a couple of issues that have been called out in the current version. Not sure when that will be of course but I will keep an eye out for it.