Perhaps someone with more experience in R-L languages can be of more help. However, from a diagnostic standpoint: you said that updating caused the reversal, implying that the originally created TOC was fine. Assuming that it was automatically created by Word, one possibility is that Word, in updating, is finding a word still tagged with a R-L language. Is this document perhaps a translation or related transposition from a R-L language, in which an editing change was made between first TOC creation and updating?

I would expect the problem not to lie in the TOC styles, but in the styles from which they are assembling the TOC. Unless the updating process, itself, has somehow gotten a switched flipped, but that is out of my league.

Best,
Ulodesk