Appending MOV files efficiently can be a challenge. The only "safe" and easy way without destroying the video or the sound is done by using Avidemux which is a free video editing tool for Linux.
Here is my modified image-convert bash script used for the appending all .MOV files in a folder and have the full video ready for editing in the Avidemux graphical user interface (GUI).
#!/bin/bash
#Inspired by http://scienceoss.com/bash-script-convert-images/
#This script will convert images to a smaller compressed format. The output files will use the APPENDNAME.STARTID=1
for f in `ls -tr *.MOV` #sort on timestamp -t and recursive order -r ltr?
do
if [ $STARTID = 1 ]; then
result=`echo ${result} --load ${f}` #Load the first file name in the folder
else
result=`echo ${result} --append ${f}` #Append all the other file names in the folder
fi
let STARTID+=1
doneavidemux3_qt4 $result
