From the OED's online entry on the interrogative form of whatever, the earliest entry for the pronoun usage as a single word is from 13—:
13.. Seuyn Sag. (W.) 3514 Son, what may al this noys be,..Whateuer sal it sygnyfy?
Interestingly, their first listed example of the two-word version is from 14—.
The first pronoun usage they have in the modern spelling:
1823 Spirit Publ. Jrnls. 409 Whatever possessed her, I know no more than the child unborn.
For the adjectival usage, the first example is in the two-word form.
c1375 Cursor M. 321 (Fairf.) Quat euer e haly gaste wille, e fader and sone wil tyte fulfil.
The first instance of the single-word form appears in 1456,
1456 SIR G. HAYE Law Arms (S.T.S.) 228 Quhatever sik men dois, it is comperit to the dede of a beste.
and, with the spelling moving through Shakespeare's contraction whatere and Milton's more descriptive Whate're (notice the apostrophe), we see the first modern-spelling usage in Swift's Gulliver's Travels.
1726 SWIFT Gulliver IV. v, It is a Maxim among these Men, That whatever has been done before may legally be done again.
Whatever happened to "what ever" appears to have started happening a long while ago.