This isn't really the right list for latex package interaction probably but the situation is I think that \footnotetextB and friends work fine in l r or c columns (so the second column in your example) If I use the code below I get footnotes bb ww and zz at the bottom of the page (sorry I added some latin letters to give my eyes something to focus on:-). Footnotes in p columns get lost (which is the default behaviour for tex footnotes inside a box) so footnote aa from \footnoteB is lost.
longtable has some extra code to "lift" footnotes out of the p-column box but it doesn't see the \footnoteB variant. It's arguable whether it should be longtable or manyfoot package that supplies the needed glue. However that does mean I think that a workaround that doesn't involve splitting the table is to use footnotemarkB in p columns and then use \footnotetextB in any l column entry on the same row. This will be a general issue with manyfoot footnotes, unrelated to use of arabic text or xetex. David %\فمب\فتب aa\footnoteB{aaفي المتن: "كشفى".}% bb\footnote{bbفي المتن: "كشفى".}% & ٣٩ zz\footnotetextB{zzفي المتن: "كشفى".}% ww\footnote{wwفي المتن: "كشفى".}text% %in the line before a FootnoteB is inserted by the commands \FootnotemarkB\FootnotetextB{}, and a footnotemark appears in the text but the text of the footnote is not displayed at the foot of the page. \end{longtable}
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