yEd Live and yEd desktop use different versions of GraphML for technical reasons. As a result, opening a live GraphML in desktop (or the other way round) is a "best effort" import that cannot guarantee identical results. Arrows in particular differ between the two applications. Moreover, yEd Live currently supports a couple of node styles that are not yet supported in yEd desktop. If you are using one or more of those styles, you will get default styles for the corresponding graph elements in yEd desktop.
The next version of yEd desktop will support those "new" styles, though.
That said, I am not aware of a shortcoming that might result in "colour code with HTML appears across the diagram" or labels missing altogether.
Can you upload your yEd Live GraphML here, so we can investigate this issue?