if you swap bits the parts will come out small unless you reapply all the cuts with the new size.
this is because the cuts are offset from the parts by half bit diameter.

 

Don't forget you can just copy and paste the existing drawing into a new area of the file and do new cutlines in the copy, then move the 'safe area' to the one you want before you generate Gcode.

also, with V1.3a you can select portions (or all) of the stuff in the safe area and only generate Gcode for the selected items.

 

go to youtube and search for 'swarfer sketchucam' and watch all my videos on the topic. (-;
not that they are perfect or the best, but they do exist and will get you started much faster than anything else.

in particular the one about using 2.5D cuts to make 3D things will help you understand the use of the safe area.

also, every tool is detailed in the SketchUcam help, which for the reorder tool says

Reorder Groups Tool - Redorder groups to change cut order
Grouped cuts will be cut first, in the order they were grouped. However, in order to edit a group it has to be exploded. Grouping it again affects the cut order.
To reorder groups select this tool and then simply click on each group in the order you want them cut.
You can use the 'Tools|Phlatboyz|Groups Summary' menu item to see the current group ordering. ​

A side effect of the above is that all plunge holes will cut first since they are 'autogrouped'

<rant> (*with smile.... sort of
programmers hate to write help.
it takes hours to write help.
to avoid having an annoyed programmer, please read the help
or in other words
RTFM
</rant>