The Apply Closest Join feature is not applicable to all objects in all circumstances. Note the following limitations.
Closest Join requires the complete stitch regeneration of the objects – the whole object, not just connectors. Stitch regeneration has its limitations:
Recognized objects – i.e. opened from machine files – may generate poor or incorrect embroidery.
Manual (unrecognized) objects cannot be changed by stitch regeneration. Thus Closest Join will not work properly for them.
Manual stitch edits to objects will be lost.
Inserted and recognized machine functions may be mistakenly regenerated on the underlay.
Nested objects are not supported. They will become un-nested and placed after the object in which they were originally nested. This may not produce ideal sequence.
The Closest Join technique is not as powerful as Branching for run objects. Closest Join will not produce a nicely-merged double-run, so connectors are only possible at the ends of the run, not in the middle. The best it can do is swap the ends of the runs.