Yes unfortunately it will overwrite. Application save data is stored inside the app itself so any time you remove/replace and app, all the data goes with it. There is a process described here using a $30 app that allows you to manually save and transfer data:
I get the whole sandbox idea and hiding the filesystem but at the very least, they can selectively keep a duplicate of save data in a safe place outside the app so that if you do need to delete/restore, you can just get all the data back again. Even if it said when you delete an app, 'do you want to keep the data' and if you hit yes, it will move the data to another location and list it somewhere like in settings. When you reinstall an app, you'd be able to restore it.
I'm with you Marvin - it'd be great if the devs would build in a save data function. There is a whole host of utilities out there tho' - some free some not. OP could search for iPhone/ipad explorer. Or learn to ssh into the device - I've forgotten all the rigmarole for ssh but no doubt it's out there in the wild. And then you need to learn the file structure of iOS ...... I still use an old copy of iPhone explorer on my PB 17 when I want to manually save stuff or hook off photos - way easier and faster than ssh or iTunes sync.
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http://www.imore.com/how-manually-transfer-app-data-your-iphone-5
I get the whole sandbox idea and hiding the filesystem but at the very least, they can selectively keep a duplicate of save data in a safe place outside the app so that if you do need to delete/restore, you can just get all the data back again. Even if it said when you delete an app, 'do you want to keep the data' and if you hit yes, it will move the data to another location and list it somewhere like in settings. When you reinstall an app, you'd be able to restore it.
There is a whole host of utilities out there tho' - some free some not. OP could search for iPhone/ipad explorer. Or learn to ssh into the device - I've forgotten all the rigmarole for ssh but no doubt it's out there in the wild. And then you need to learn the file structure of iOS ......
I still use an old copy of iPhone explorer on my PB 17 when I want to manually save stuff or hook off photos - way easier and faster than ssh or iTunes sync.