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If you wipe data and cache, bye bye boot animation. But if you're upgrading Cyanogen (which I would guess you are running, considering you have a Cyan boot animation) there shouldn't be any problems with losing your ani.Nice work!!
I just used terminal emulator to install mine. Here's what I did.
Mount your filesystem as r/w (I used Droid Root Helper)
Open Terminal Emulator
$ su
Allow Root (if applicable)
# cp /sdcard/bootanimation.zip /data/local/bootanimation.zip
Its pretty trivial if you're familiar with Linux command line operation.
$su
#mv /sdcard/bootanimation.zip /data/local/bootanimation.zip
#reboot
using the move command, it will no longer be on your SD card after applying the new bootanim. Just be sure that bootanimation.zip is in the root directory of your SD card.
EDIT: Actually, you do not need to mount your filesystem, considering mounting mounts /system and not /data.
I chose to keep it on my card because I wasn't sure if its going to survive a ROM upgrade in the future. I'm not too familiar with the filesystems that are r/w and what aren't. Thanks for the info :icon_ banana:
How do I go back to the original bootanimation if I already installed this using terminal emulator? I don't have root explorer.