You do need to close any character styles in footnotes, including \xt …\xt* and \em …\em*. However you also need to change these to embedded character styles, in other words you should use \+xt …\+xt* and \+em …\+em*. This will ensure the text displays correctly in your Paratext browser and eliminate the error saying that you have an empty \ft.
For cross references in footnotes you should do this:
\f + \fr 1:1 \ft Text Text \+xt Ref. 2:2\+xt*. Text Text.\f*
(Nerd Note: All footnote specific styles, those beginning with \f , \fk \ft \fq \fqa do not need to be closed because Paratext automatically closes them before starting the next style.)
For emphasized text the markup is basically the same:
\f + \fr 1:1 \ft \+em emphasized\+em* Text Text Text Text.\f*
Do not use \fk for bold because it is intended to mark key words in the text that are also in your footnote that you want formatted in some special manner.
Now if what you are emphasizing is an alternate translation, you should actually use \fqa … The text after \fqa is not checked against the text in the translation. For example:
\f + \fr 1:1 \fqa Emphasized \ft Text Text Text Text.\f*
If you would like to see some more examples of various kinds of markup in footnotes, I would refer you to the NIV resource in Paratext. There are a number of different variations in its 2000+ footnotes.
CrazyRocky
Biblica