I suspect this trouble is trailing from previous versions, although recently checked in 4.0 and 4.1:
-insert in your epub a svg containing clones
-check in book-edit--no trouble (same in Sigil)
-open in e-viewer: only the originals of the clones show; all clones become invisible.
Attached small test epub with several tests of the issue; one of them generates warnings (unhandled exception).
I suugest opening TestSVG.epug in edit-book or Sigil->Preview and comparing with the rendering in Ebook-viewer.
Should I open a bug report?