I know this may seem dumb, but I have been losing my game development progress every time I tried to add the new, updated files (copying and pasting over old project files with new project files). How can I update my ARPG project without losing my files like imported tilesets and new maps created?

All you need to import is only the plugins in the plugins folder of RPG Maker Action Combat. You don't need to import anything else. Overwriting the plugins alone won't break anything, unless the plugins change how a feature from themselves works. If that's the case, you'll just need to adjust that plugin command from Action Combat in your project. It doesn't always happen, but if it happens, it's unavoidable because the plugins have to grow so they become better and better. Overall, import just the plugins and it's safe.