First of all thank you for replying

Perhaps a more full explanation would clarify things.

I have a php script installed that will allow clients to download files to any folder that I have given them permission to, when they go to folder 1 and open it there are around 60 files available for them to download individually, originally if they wanted the whole folder downloaded they would select the folder and then when the download button was pressed, the folder was then zipped, and when zipping was complete it started to download as one zipped file. problem is that if there are a lot of files in the folder the script times out.
I have maxed all the relevant settings in my php.ini file and the problem sill exists.
Downloading each file individually works well if you only require a few files, but when you need the whole 60 it becomes impracatical - so, my work around was to have all the folders that have loads of files in them, zipped and relocated to another place on the same server so as to give the clients the option of downloading one big zip file containing all the files yet still download if required from the original position on the server the individual files.
As new individual files are being added every few weeks and old ones removed, it would need the zipped file to replace the old one with itself as to always have the most recent available for download as one large zip.

Copying the folder with lots of files in it, zipping it and dropping it onto another location on the same server is important, as I would have to set permission to download the new zipped file to whoever wanted access from the script on that server.

Hope I made things a little clearer.

The php script is 'Secureloads'.

Not sure what you mean when you say "Can you tell us more about your Linux distro?"