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[thejflo]

Before I'm about to install 1.4.13, I want to make sure so I don't have to bother you guys again if I make a dumb mistake like I usually do (lol).

For example:

I have extra themes (some made by me) in the current version that I added. The new version has the basic themes that always come with the pack (of course). Does this mean, for example, that I do not have to re-upload the new "themes" folder (so I can keep my old one that has the themes that I've made)?

[Joachim Müller]

Each of your custom themes should reside in a folder of it's own within the "themes" folder. Copy those individual sub-folders (e.g. http://yoursite.tld/your_old_coppermine_folder/themes/your_custom_theme_1/ and http://yoursite.tld/your_old_coppermine_folder/themes/your_custom_theme_2/) into the themes folder of your new install (e.g. http://yoursite.tld/your_new_coppermine_folder/themes/).
Do so after your initial install has been successfull.
For details, post details (links usually help best).