Without an MWE, I can only guess, but my guess would be that you’re using the actual unicode character “℣” (U+2123) and while Linux Libertine defines that character, Libertinus does not. It’s for fonts like this that Gregorio defines \Vbar, though you might need to tweak it to make it look good. See the section on Barred Letters here:
http://gregorio-project.github.io/gregoriotex/features.html.
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Fr. Samuel, OSB
(R. Padraic Springuel)
St. Anselm’s Abbey
4501 South Dakota Ave, NE
Washington, DC, 20017
202-269-2300
(c)
202-853-7036
PAX ☧ ΧΡΙΣΤΟΣ
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