Next time, please stick to your original thread for follow-ups.
Scaling does not affect margins. Scaling is a yEd setting that - well - enlarges or shrinks your diagram on printing.
If scaling is set to "Automatic" your diagram will be scaled to fit the print size (print size is paper size minus the margins reserved by your printer). I.e. diagrams that would take up less than the available space will be enlarged and diagrams that would take up more than the available space will be shrunken. Please note, that automatic scaling does not result in a "tight" fit, that means the scaled diagram will usually take up slightly less than the available space.
If scaling is set to "User-defined" the given scaling factor is applied. E.g. suppose you are printing a single node with width 72 and user-defined scaling factor is 1, then the node's printout will be 1 inch wide. If you change the scaling factor to 2, the printout will be 2 inch wide.
That said, I am suspecting that your graph is actually shrunken to fit the print size due to automatic scaling. If your graph is either wider than 468 or higher than 648, its size has to be reduced to fit onto an 8.5" by 11" paper with 1" margins (resulting in a print size of 6.5" by 9").
(Original thread was copying & pasting graph to "new" and renaming: modifying changes margins)