I have been working on a Magento site remotely that is now ready to go 'live' (it was worked on remotely as to not make any changes to the live site until it's ready).
I plan on putting all the 'app' / 'media' / 'skin' etc folders back onto the server with the new changes, and will make all the backend changes manually as I want to keep the recent orders and database that has been created.
However I would like to do the update to Magento before doing so. I know that Magento updates often overwrite the 'Core' files. If i'm replacing these with those that I have externally anyway, will it matter? I guess my concern is that the files I upload won't now be compatible with the update that I plan to do.