On what basis do you say the aup files were corrupted? Because Audacity won’t open them? Is it worth attaching an AUP for us to see?
Generally (in my experience) Linux and Windows won’t read zip files created on the other operating system very well if you are sending them across a network - it is some kind of encoding incompatibility. Use FTP to and from a server, or (possibly) try a USB stick.
If you need to piece together the AU files the instructions on sorting and renaming the files are in the big green box here http://wiki.audacityteam.org/wiki/Crash_Recovery#Automatic_recovery_tools .
So, if you are going to recover on Windows, use the instructions for xplorer 2, and then use Audacity Recovery Utility.
If you recover on Ubuntu, open a terminal then cd into the directory that contains the au files.
Then type:
mkdir "renamed" | find -type f -name "*.au" -printf "cp %h/%f renamed/%h/%TY%Tm%Td-%TH%TM%TS_%fn"|sh
and hit ENTER. This should sort the files numerically in time stamp order, so that when they are sorted in ascending numerical order (lower numbers first), the files will also be sorted in ascending time stamp order (the files that were recorded first should be first in the list).
The Audacity recovery utility cannot use those files because it wants a continuous alphanumeric sequence of files. So either:
- Use Thunar to rename the files as they are now sorted into a continuous alphanumeric sequence and then use the Audacity Recovery Utility
- Use the Nyquist Append Import plug-in to import the files as alternate channels.
To install Nyquist plug-ins, see here http://wiki.audacityteam.org/wiki/Download_Nyquist_Plug-ins#install .
Gale