It seems after upgrading to 5218 I cannot figure out how to get the Code Navigator to function in single file mode? I used to be able to right click and select "Single File" but that option is no longer available.

Code Navigator does always operate in single file mode and this mode can't be changed there. Probably you referred to Code Explorer, where you indeed could change the mode and you still can change it, except "single file" mode which is represented with Code Navigator now.

You are right, this is a case of user error: turns out that after I updated to 5218 my Code Navigator button disappeared, and on the left hand side the Code Explorer showed up. This got me confused.

I guess this might be another item that is lost when updating (the placement of some of those toolbars).

it might happen only if you did overwrite layout.cfg file with one you had for previous version which of couse did not contain any info about Code Navigator and therefore the buttont would not appear.