Mantra 1.9.9.3 is a very old release. We implemented multiple design and layout tweaks and changes in both the 2.0 and newer 3.0 release. We did these changes to optimize the functionality and structure of the theme, to bring it up to date with browser supports, HTML 5 markup and also some current design trends.
These changes are part of the theme and will slightly change the appearance (mostly concerning font sizes and spaces/paddings) of your site after performing the update – there’s no way to avoid them except to undo them all manually (by customizing a lot of the styling).
Beyond these changes (font sizes and spacings) nothing else should change due to the update. What other changes did you notice?