I certainly would not overwrite the default common.js, because this will affect the default template.
Make sure you compare the 2 files first. If your theme file is identical to the default one with only added scripts, then it should be ok to overwrite. If they are substantially different then what I would do, is to rename the .js from the new theme, like this for example "commonTheme.js", and change/add the call in the header.tpl of my new theme.
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Just ALWAYS rename the default common.js into d_common.js (and other Custom Theme changed key-files!), to still have it, before you upload such an Extension/theme, containing ANYTHING, not only the common.js, placed OUTSIDE of the THEME Subdirectory, in case, you decide on removing such Themes again. If everything works well, you could later remove such 'd_'-marked Spare Files out of your Software for good.
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