Yes, you are correct that you can't have a parent and child portal with the same name. We would recommend deleting the Sub Domain from Helm and make sure that the corresponding sub folder within your domain's folder system was removed. Also delete any Parent or Child portals currently setup within DNN. You originally did the Parent Portal setup for "uk.mydomain.org" correct except that you created a Sub Domain within Helm instead of a Domain Alias. When creating Parent Portals in DNN, you always want to use the Domain Alias option within helm instead of the Sub Domain option. Domain Aliases resolve to the root folder of your domain where DNN installed. Sub Domains resolve to a sub folder within your domain's folder system where DNN files do not exist. Hence why it would not work previously while using a Sub Domain in Helm. Simply start the procedure over and do exactly as you did before only create "uk.mydomain.org" as a Domain Alias instead of a Sub Domain in Helm and it should work exactly as you intended it to.
You could do this before or after upgrading your DNN version. Any portals on the installation would be upgraded along with the core DNN installation during an upgrade. However, we replied to your other forum post in regards to upgrading your DNN installation. As we stated in that post as well, we would recommend contacting our technical support staff in regards to your domain's upgrade before getting too far in development. It maybe easier to do a reinstall of DNN 5.2.2 than an upgrade. Depending on what version you are currently running and how far you have gotten in development. Our staff will help you decide the best way to proceed on getting your site's DNN version up to date.
You are always welcome to post questions like this in the forums but we cannot guarantee our staff will always be able to reply promptly. However, other community members may offer assistance. If you wish to ask questions directly to our technical support staff you are always welcome to submit a support ticket to us at the link below or at https://support.ihostllc.net.
Submit a Support Ticket to iHost Support Staff:
https://support.ihostllc.net/index.php?_m=tickets&_a=submit