Are you sure you edited the right eqp files? Also, don't just copy and paste, not all of the subs have the flags in the same equipment spot. For instance, the VIIc has them listed in the 14,15 and 16 spots.
Find the line in the NSS_UboatXXX that starts "; Edited by TheDarkWraith" those usually say flags in their name. All you have to do is change the start date to 19380101 in order to have them from the beginning.
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