Hi Eric,
If I got you right, you want to change the size of the text in your annotation layer without actually modifying the underlying attribute table field (i.e., FontSize field). This can be done within the symbology settings of your annotation layer in ArcMap. Right-click the layer > Properties > Symbology tab > Symbol Substitution > Substitute individual symbols in the symbol selection option.
Symbol Substitution is layer-based functionality for temporarily changing the symbology of an annotation layer in ArcMap and these settings are stored within the .mxd document, but you can export a layer file (.lyr) which will preserve the symbol substitution settings, too.