In addition to using Mark Hubbard’s “Thank you in advance for [keeping me informed]” (or just “Thanks in advance for [ … ]” in less formal situations) to express your thanks in advance without having to rely on context, you could also consider using a near-synonym for being thankful to use with the conditional would, for example:
“I would (I’d)[ greatly/very much] appreciate your keeping me informed.”
or (to emphasize the conditional notion even further):
“I’d be [extremely/very] grateful if you would (you’d)/could keep me informed.”
(Please note that, although it’s probably overstating the actual level of appreciation/gratitude, I think I would include greatly and extremely, especially in the above, “in advance” cases, but probably less so in the “after the fact” cases mentioned below. However, be careful not to “over-do” it because you could come across as being sarcastic or “sycophantic” [the English sense!], so on second thought, maybe the more restrained very/very much would be better in these cases where intensifying the gratitude might be in order because you are actually requesting a future favor at the same time.)
Regarding “after the fact” expressions of thankfulness (such as the one you made on “Overflow” and are asking about here), in addition to Mark’s use of the past tense (provided) or relying solely on context (which I agree can be ambiguous, especially in your example where it could easily be interpreted as an on-going request), you could consider changing “keeping” to “having kept” and “keep” to “kept” to use either with the same near-synonyms above (but in the unconditional present) or else (preferably, I think) simply with the original “Thank you/Thanks” construction, for example:
“I [do] [greatly/very much] appreciate your having kept me informed.”
(where the do would be an optional way to emphasize the appreciation)
“I am (I’m) [extremely/very] grateful that you kept me informed.”
Thank you (Thanks) for having kept me informed.
(But please see this relevant Word Reference thread that seems to confirm that we are, in fact, often (but not always?) at the mercy of sometimes ambiguous context in English (as indicated in user3169's answer). At least “Kelly B” begins his/her answer with “Yes, that's right,” so making the effort in our own speech to avoid the ambiguity would be not only admirable, but also grammatically and logically correct, although we'd still have to rely on context to interpret the meaning when spoken to us by somebody who is less concerned with clarity.)
Best Answer
You can think of "see you" is a short form of "see you again soon". It doesn't matter whether you are currently with them, because you have probably seen them at some point before, even if you are not with them now, and it's about the next time you see them.
Arguably, you could still say it even if you expect your next contact to be by phone or email, because at some point after that you probably will meet them face to face again.
If you want to make it clear that you expect to be in contact with them by some other means (phone, email) then you can say:
Note that the written form is rather more formal... it is more suitable to finish off an email than to say to somebody directly or by phone.
I have even heard expressions like "Skype you soon!".