The instructions say to capture inverted (upside-down) letters, assuming that they are recognized as such, as if they were turned upright. Some examples:
Inverted ligatures should of course be turned upright as a block, not letter-by-letter. E.g. an inverted "ae" ligature should be turned upright and captured as "ae" not as "ea"; and inverted "ct" ligature should be righted to "ct" (not tc); etc. This example is from Wh3124.
And spans of letters or words that are printed upside down should (again of course) be righted in the same units in which they were inverted, so as to restore intelligible text. E.g. in this example from S15217.5, the number in the lower right should be restored to "3567":