I went ahead and looked at this for 2 mins.
Using https://wikidata.beta.wmflabs.org/wiki/Lexeme:L1 and L1-S3 as an example
I noticed that the property P730 was pretty old, originally being created in 2014.
I edited the label https://wikidata.beta.wmflabs.org/w/index.php?title=Property:P730&diff=1050777&oldid=26249 and then it started appearing back on L1
I also changed it back https://wikidata.beta.wmflabs.org/w/index.php?title=Property:P730&diff=next&oldid=1050777 and it continued dispalying on L1.
I assume this is just some really legacy stuff / beta problems and I don't think it is a bug with Wikibase ot WikibaseLexeme
I imagine the other 3 links are similar cases, but I have not checked myself.