If you get this kind of warning there are two ways to get rid of it.
1. Way
If you changed all your links to the "new", generic links, then just use the variable name of the input component.
2. Way
If you still use the "old", static links, then the warning appears, because the method #link.comment has been marked as "deprecated". The comment-field of a link has to be filled, else the warning occurs.
So you need to change your query from
$CMS_IF(!#link.comment.isEmpty)$
to
$CMS_IF(#link.isSet("comment") && !#link.comment.isEmpty)$
Explanation
The mentioned method is overwritten within the object, but the new method needs a comment. So you need to prevent a method call, when the comment is empty.
Hint
It is possible that the section and the language of a link causes the same problem.
