What does FontLab do with font-level TrueType hints? Do your current products preserve the font-level (TrueType) hinting? This is what would be necessary to import a super-hinted TrueType font, re-arrange glyphs, and preserve the total hinting.
1. If "Save TrueType hinting information" (in Import options) option is on, then it stores all hinting data at file open time: PREP, CVT, FPGM, HDMX and glyph programs (but not VDMX). However, editing glyph outlines will delete the glyph-level instructions for that glyph!
2. If "Keep existing TrueType instructions" (in export options) switch is on, all hinting data previously in the font is maintained. Remember that glyphs that have been "touched" (any point is moved, inserted or deleted) lose glyph-level hinting data. Font-level hinting data remains until no characters remain hinted. Also note that the VDMX table is not stored in any way.
3. If any of characters have visual hints, or the autohinting option is on, then FontLab's font-level hints are added to original hints (if they were saved at file open time), or only FontLab font-level hints are exported. If font-level hinting data is added, then special commands are used in each character-level instruction to avoid interference between two sets of font-level hinting. This makes fonts bigger by 1-2%, and in some cases decreases font rendering performance a bit. So, if you redo TrueType hinting for most of the glyphs in your font, we generally recommend to not keep the original hints.