I would think that Penny would
consciously acknowledge the alteration Desmond made to her life, because she didn't change her number and she waited for him - crucially, she remembers their conversation which future Desmond 'implanted' into her when he came to her house and begged her not to change her number etc.
For me, this is proof that Desmond's time-travelling implants new experiences into the lives of those her encounters, whilst 'past-Desmond's' memory has been wiped over with 'new memory'. The suggestion could be that past Desmond is not aware of what is to come, but experiences some 'sensation' - some call it "destiny", and this could well explain why the Des who meets Jack in the football stadium seems to have a sense of purpose and a sense of 'knowing' without 'actually' (consciously) knowing..if you get me?
I think that crucially the key aspect of all this is 'perception', and the perception of time. I have a theory that you can affect others through time-travel, but you can only perceive to affect yourself, since one cannot have two independant minds in two places in time at once, but you CAN have one unconscious mind and one conscious mind.
Is this what 'destiny' is made of..the sense of having to do something..of being 'supposed' to do something?
Quite possibly..
(just my interpretation, could be wrong)