When adding an obsidian plate to a tool that used one on it's making, not only it adds a level on reinforced to the tool, but also replaces the plate of the tool. Not sure if there is a way to fix this other than to change the item for the reinforced modifier.

That can't really be fixed due to how things work. Just use an obsidian plate, apply all the reinforced, and switch it back to the material you want.