The next time you restart your browser, the update will be applied.
As an example you may not be able to write an image of a 64GB micro SD onto another 64GB card.
It can also be accessed from the terminal with Core Packages Each section of the manage packages portion of the setup script have the option to install/update all packages and remove all installed packages.
You can also update/install and remove packages individually.
The core components needed for Retro Pie to function are: You can update/install and remove packages individually.
When selecting a package there is also a help guide with extra information specific to that package: Package Help: The Package Help for each emulator should show you: If you are worried about conflicts during an update you can always just start with the latest fresh sd image which can be downloaded here and just copy all your files back over onto that instead of updating from an older image.
A possible work-around would be to attempt to update your console at a more optimal performance time, such as early in the morning (2AM - 10AM), as you are more likely to encounter a receptive updating time with people at school or work.