Though I have not cross-checked, as far as I understand, most of the online companies providing such services (such as whatsapp) save the conversations for their own safety to protect themselves in future court cases, though of course, the conversations may be saved only for a limited duration. Now that Whatsapp has been taken over by Facebook, there is all the more reason to believe that such conversations on whatsapp might perhaps be saved on their servers at least for a limited time period. In fact, even the mobile phone companies save all the SMS messages sent over mobile phones for a reasonable period (I think it is for one year or so).
Moreover, usually whatever content is downloaded / uploaded from or to the Internet is NOT encrypted. When you login to a secure website (HTTPS), the login details are encrypted when they are transmitted to the server, but further communication (i.e., after the login) may or may not be encrypted. Moreover, even if such further communication is encrypted, it may be stored on servers and can perhaps be decrypted when requested by the law enforcement agencies or the courts. There is a difference between login details which are encrypted using HASH functions (which use one-way encryption that cannot be decrypted) and other communication which is encrypted using normal encryption algorithms.
In any case, presuming that such whatsapp messages are not saved anywhere (either on whatsapp servers or by the ISP or by anyone else) and also presuming that such messages can be tempered with by the user, in that case their evidential value will be reduced greatly and it can be proved by the concerned party to a litigation that such conversation was tempered with.
Regarding your second query asking me to explain my last statement in my previous message, let me point out that under the Evidence Act, there are limitations as to what would be allowed as evidence. Not every fact can be considered to be “evidence”, and moreover, evidence can be tendered only in the ways permissible under the Evidence Act. Further, once certain “evidence” has been adduced in the court, it does not mean that it will always be considered by the court to be “gospel truth”. There may be counter-evidence. For example, the statement of a witness before a court may be evidence, a document exhibited before a court may be evidence, but whether or not such evidence is reliable, truthful and trustworthy, will be decided by the court by analysing it along with all other pieces of evidence adduced in that case. Therefore, “admissibility” of evidence is one thing, and its “reliability” is quite another thing. It is in this sense that I had stated in my previous message that “(h)ow much reliable or trustworthy or how much weight is to be attached to them, will be of course a subject matter of appreciation of evidence”. I hope I have made myself clear on this issue.