Multiple instances (having >1 cura.exe open) is a problem with Cura. Multiple instances is necessary if I e.g need to adjust a gcode and re-print. Having multiple printers and working on multiple projects, I often need multiple instances.
This commonly leads to what I guess is de-sync within the settings of Cura. It messes up the files, and the easiest way I've found to get things working again is to delete all %appdata% and manually adjust and insert settings everytime this happens, which can occur many times a month.
My suggestion? Implement tabs like photoshop or every web browser and figure a way to sync while having multiple projects open. This makes it possible for users to work on multiple projects without having 5 cura.exe open.