Prob my last LOST theory ever.....nah! it's just been a bit of a long time....
Back in season 1 and 2 when Claire was kidnapped and taken to the "medical hatch",she lost her memory and was very "foggy" with recalling everything that went down. Yes, we clearly see Ethan make sure that Claire kept drinking from the canteen with the "Water' in it(I'm sure it was some type of roofies in there)...but....after watching LOST: the complete series box set! THAT I OWN(YEAH)!!!!....Room 23 is clearly explained to us(and it was a good enough answer for me), and it made me think about Claire.....
I feel that at some point after Claire was taken and before Alex helps her escape-Claire was put into room 23 and "wiped"....
...but she eventually recalls escaping?
I think it works like this....
Claire does not remember being on Hydra Island and Room 23 due to the fact that the "brainwashing" effects of Room 23 had a very strong effect on her-and all the time being taken and being on Hydra Island would be "wiped" from her mind....
..but...from the time being at the Medical hatch-she would be able to eventually recall her time there due to the fact that Ethan might have used a milder drug to "dope" her up(She was acting very loopy and submissive).
The reasoning of this theory is because the "Others" kept the Room 23 procedure as standard "protocol"(this was shown with Walt and Karl). So with everything we know now, I think it's safe to say the Others also did this with Claire.
Enjoy, Folks!