A mesorah records that the samekh in Bemidbar 13:30 ויהס כלב is large (see marginal note in Artscroll and elsewhere). Yet none of the printed editions which I have consulted actually conform to this tradition. Have you come across any info on this?
Interestingly enough in Torah Shleimah Vol 29 which discusses the unsual letters in the Torah - ָכתַב התורה ואוֹתִיוֹתֶיה - I can't seem to find a reference to this enlarged ס in either of the lists nor with a (possibly unreliable) text search.
The Keter site doesn't have anything about the ס either on this verse.
And The Minchas Shay says that in reliable texts it is not large, though he mentions 2 sources that seem to have it enlarged.
ויהס. בספרים מדויקים כ"י אין הסמ"ך רבתי גם במסרה גדולה ליתי. ואיתא בדוכתא סמ"ך סוף ספר קהלת
אכן בנוסח אחר כ"י מאלפ"א בית"א רבתי איתא וכן בתיקון ס"ת ישן.
This list does include it with 5 references mentioned.
I think the answer to the question is that there is no agreement as to whether the samech should be large. I thought it was universally agree eg the ayin and dalet in the first paragraph of shema. –