Im curious too, which you are trying to flash?
I have 2 themes post here, and both have good workin update.zip installs, as well as instructions to manually install them via ADB Recovery.
to answer the OP question:
Themes are merely editing the original "drawable" files, or Pictures, in a given apk (program)
Both methods of installing my themes simply over-write the original files with "themed" duplicates. The files actually edited do not in anyway affect the filesystem, therefore should not cause adverse effects. If your having issues with a particular theme contact the theme builder, they would have the most pertinent info, and best solutions to you problem.
If your problems are from flashing a ROM, then essentially you are wiping your filesystem and installing a completely diff version. ROMs are copies or modified versions of the Android operating system. If the ROM builder made a mistake or did not build it properly, the adverse effects are countless. If you have a "bad ROM" you would need to reflash with a known good ROM, or recover with a backup. (hopefully you made one prior to jumpin in.