I had this same problem with disappearing field values in flex fields I had added to my existing flex field UIBB. As others have stated, SMT mapping is not applicable to flex fields.
I tried running both USMD_ADAPT_BRF and USMD_ADJUST STAGING with no results. I finally resolved by running BRF+ transaction USMD_RULE and making sure I specified a transport for BRF changes rather than choosing Local object. It then clocked for a while as it was obviously regenerating the structures. Therefore, it seems that unless you have an open transport, running program USMD_ADAPT_BRF (or simply opening USMD_RULE) may not actually regenerate and save.
Rob