Hitting Save currently makes the Projucer export to all target platforms at once, overwriting whatever manual changes have been applied to individual platforms. I often find myself refining a particular platform, while I don’t want an export to “reset” all the other platforms, effectively undoing previous fixes. This already nuked hours of work in a second.
Please consider adding an option to the right-click menu to save a particular exporter only. This will greatly help with refining/fixing each target platform individually.