Soul Crystal Extraction, fees are unknown until they fix the process.(you will recover the Soul Crystal used for that SA, but nothing else, no R-Gem)... which will allow you to re-apply the same SA with a higher level Soul Crystal(you would need to Replace/Overwrite 2 times ie. change Might 4 > Body 1 > Might 7 before Extraction was possible)
Soul Crystal Replacement(Overwrite) is used to change an SA to a DIFFERENT SA, you loose the original Soul Crystal without any recovery possible(ie. change Might 4 > to anything besides Might [any level])
1st and 2nd Soul Crystal same expense(R-Gem) is the Big change... all R/R95/R99 same expense is HUGE CHANGE(anybody with 1SA R95/R99 used to be frugal/poor... now if you don't have 2 normal SAs maybe some random party you join could help you out)