Step by step guide how to reproduce it:
1. Create new project, add an array to layout, set the dimensions of the array, add any events to the sheet (optional), save project, close project, reopen project.
2. Make changes in the array dimensions via object properties window (btw, there's little sub-bug - object properties changes don't make save option available), make some changes in the sheet to enable project save, save project, close project.
3. Reopen project. Ta-da! Array changes didn't saved.