Decompose should apply to all glyphs in the typeface so as to avoid unexpected component swapping. Remove features presumably does nothing to the actual glyphs? And Rename Glyphs contains this relevant line:
llinebelow.ss01=llinebelow
Both of these glyphs exist, so I don’t see how one of them could get lost.
I recently had trouble with /rlinebelow, which decided to rename itself /rmacronbelow unexpectedly, but llinebelow doesn’t seem to want to do that when I use Update Glyph Info on it.