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Okay, so what I have right now is I upload my files, it unzips them, everything works fine.
What I'm having trouble with is how to upload a zip file (Which is the same name as a directory), and the contents inside the zip file replaces the contents on the server that has the same name.format and keeps all the other files the same.
Your question is very unclear so it's very hard to answer you. What are you trying to upload? Where are you trying to upload it to? A zip file is like any other file with respect to uploading and downloading. What is different is what you do with it. If you are uploading it then the person you're uploading it to is the one who will unzip it. Is this what you mean?
Please look up the definitions of "upload" and "download". Do you really mean?
User uploads a game to their directory (/home/user/hostgames)
or do you mean "downloads" in this case. You upload from your computer to somewhere else on the web (e.g. Google - "I uploaded my contact list to google"). You download from somewhere to your computer. Using these terms correctly will greatly increase the chances of a helpful answer.
Before you upgrade the game why not rename /home/user/hostgames/solarconquest as /home/user/hostgames/solarconquest.old. Delete the .dmb and .rsc files from this folder. Now you can do your upgrade. Next delete all the files in the new .../solarconquest folder except for the .dmb and .rsc files. Now copy all the files from .../solarconquest.old to .../solarconquest.