This used to work in older versions of Shotcut because size and position info was saved used percentages, which would scale when you changed the resolution at export time (but it never worked for HTML-based filters because HTML is not such a simple thing to go into programmatically and adjust everything). Since the introduction of keyframes, Shotcut needed to start using some different APIs that is now saving the information using pixel values. I am aware of this and am working on a fix to save using percentages again, but I do not yet know if that change will make it into the next release v18.08 due next week. In the meantime, the general rule is - with a timeline-based project do not adjust the export resolution and best to set Settings > Video Mode at the start of the project.