It looks like any HTML components set with Appearance: Margin type = None fail to appear when an App is reopened after editing, in either edit or preview mode. The only way to make them visible is to find them in the Component tree, as it doesn't seem possible to click on them in the main canvas. There are no issues when Margin type = Normal.
Circling back - this was fixed in the Retool Cloud release at the end of September, noted in these changelog notes under "Fixed an issue where the height of HTML components were set to zero."
@ash-c thanks for reporting this, and thanks @mckenna for chiming in and making the fix!