It seems that the new line/returns (LF/CR characters) of annotated text are written into the compiled output, even if the annotation text itself is not. Depending on how much text is in the annotation, this creates big blank holes in the compiled text.
Try this example text:
Line to stay
Line not to appear in compiled output
Line not to appear in compiled output
Line not to appear in compiled output
Line not to appear in compiled output
Line to stay
Now format the 4 “Lines not to appear…” as annotation (Shift-Ctrl-A).
Then compile. The output will contain 4 blank lines between the two “Lines to stay”.
I am trying to reduce a 400-page text by cutting out a lot, but want to do the cutting non-destructively, so I can change my mind about what goes into the final text and what not. So I format whatever I want to cut as annotation. This seems to work, except that the source text contains pages of poems and songs, their lines obviously ending with line feeds, which when turned into annotation all result in long runs of blank lines in the compiled output!