Run this script on linux.
Modify the "find" call and the source encoding.
The example will match all .java files in the current folder and its subfolders and converts from Cp1252 (Windows) to UTF-8.
#!/bin/bash
# modify this find call for your needs
list=$(find . -type f -name "*.java")
for item in $list
do
echo "Item: $item"
# change source and target encoding here
iconv -f Cp1252 -t UTF-8 $item > ${item}.x
cp ${item}.x ${item}
rm ${item}.x
done