The reason that a copy is left in the Calibre library folder is so that next time around you do not have to take the overhead of recreating those files.
However if you are using Dropbox, then you are probably best of using the options on the Advanced tab to not generate tailored images for thumbnails and cover images as described at
https://wiki.mobileread.com/wiki/Cali...g#Advanced_Tab. If you change the settings to use the Calibre cover images then the next run of Calibre2opds will also remove the tailored ones that are in the Calibre library.
Just to check - I assume that you do not have the Calibre library itself under Dropbox? Just checking as if that is the case you do not need to use the Publish mode but can instead simply use the Default mode which generates the Calibre2opds catalog as a sub-folder of the Calibre library folder.