There are two bugs actually: 1) Create .kra file and mark it read only 2) Open it in Krita Krita's title bar tells "file is read only", which is correct 3) Press Ctrl+S. Krita silently overwrites the file. Bug1: Krita should ask the user whether he wants to overwrite a read-only file or choose a different name/path instead of silently overwriting it. Bug2: Krita's title bar still tells that the file is read-only (whereas it is not) and modified(!). 4) Press Ctrl+W to close the document Bug3: Krita asks whether to save a modified file, but the file is already saved.
This is fixed in the meantime, with Agata's work.