In my project there is a broken reference to a JAR file that missing (and this error message is correct). (see screenshot 1).

Now, when I add a replacement JAR for the missing JAR file via the project properties window then the "Add JAR/Folder" dialog is shown where I can add the JAR file via its "Relative Path", "Path from Variable" or "Absolute Path" (see screenshot 2a). ...and when "Relative Path" is chosen then in "Libraries" the path to the added JAR file is correctly relative (see screenshot 2b).

But, when I instead use the "Resolve Project Problems" dialog (see screenshot 3a) then I only get a regular filechoser to chose the JAR(see screenshot 3b), i.e. without possibility for a relative path as above, and thus JAR is also added to the "Libraries" with its full (and not relative) path (see screenshot 3c).