In Substance Painter you can just change the blending mode of the layer above to overwrite the height information. By default the blending mode is set to "add" for the height channel. To change the blending mode see : https://support.allegorithmic.com/documentation/display/SPDOC/Blending+modes
Exactly as Froyok said but don't forget to switch from base colour to height from the channel dropdown(else you will be changing the blending mode of the base colour)
if you want to override the bake, you need to set the Normal mixing mode in the texture set settings to Replace so that content of the layer stack can replace the bake instead of just being added on top.
there is also one thing that I missed (in my case) - some materials do not have Height or Normal channels enabled by default, so changing the blending mode for them doesn't work. After I enabling these channels it worked.