There are different Hebrew definitions for the word "overthrown".
The version used in that verse was of change, not destruction. There are other definitions for destruction.
As Evmur said, God changed the Ninevites. We can know this the correct interpretation of the word
since they were changed but did so only by God's moving in them to do so.
Therefore, God did exactly what He said He would do: there was no contradiction nor conflict in either what God said or did.
This is the definition of overthrow as used in the verse
Overthrow:
Transliteration
ḥāram
- to turn, overthrow, overturn
- (Qal)
- to overturn, overthrow
- to turn, turn about, turn over, turn around
- to change, transform
- (Niphal)
- to turn oneself, turn, turn back
- to change oneself
- to be perverse
- to be turned, be turned over, be changed, be turned against
- to be reversed
- to be overturned, be overthrown
- to be upturned
- (Hithpael)
- to transform oneself
- to turn this way and that, turn every way
- (Hophal) to turn on someone