Since layout calculations do not affect font sizes in any way, I guess "resetting the layout" increases the distances between nodes and edges to prevent these from overlapping the larger labels. Due to the larger distances between graph elements the graph's overall bounds increase and yEd's editor area needs to zoom out more to completely fit the graph inside. (The same is true when printing to a fixed paper size.)
I am afraid I do not know a good way to handle this situation.
You could try not resetting the layout after increasing font sizes.
Another option would be to export your diagram to a vector format such as PDF or SVG. Viewer applications for these formats (like e.g. current internet browsers like Google Chrome or Mozilla Firefox) offer the possibility to zoom into the displayed document. Thus you could keep your (relatively) small font sizes and zoom in when needing to read your text.
