I have a similar issue after the upgrade as well, except I just see a cursor block and not %

macOS 10.14.4
Hyper 3.0.2 (stable)
Oh My ZSH

Hyper:

Terminal:

duplicate #3586

It seems like this is a zsh specific issue. It has to do with partial line preservation and, theoretically, should output to either % or # depending on the user running the prompt (i.e. user = %, root = #). For some reason when the user's shell is zsh on Hyper's initial init, something is being run that creates a line in the prompt that does not end in a newline. I've been working on a PR that fixes this for Hyper, but haven't found an elegant solution yet. In the interim, edit your ~/.zshrc file to include PROMPT_EOL_MARK="". Then, either restart Hyper or run source on your ~/.zshrc. This removes the % sign. However, it does not clear the newline the % held. Running clear or reset will set the prompt's cursor back at the top.

@rauchg @chabou @leo @matheuss since you all seem to be the top contributors for Hyper, perhaps you could best aid in crafting a solution for this problem by providing a bit of development context.
Describe the lifecycle of Hyper. From Initial launch => loading configs => render of prompt => etc. => until final "ready" state where the user can begin interacting with the prompt. If you could provide the location of the code that executes each state, that would be helpful as well. Cheers.

This should fix it: Adding unsetopt PROMPT_SP to .zshrc

Update: Closing because of duplicate