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...per your comment on the question...

pax -rws'|\.JPG$|.CAP.JPG|' /root/of/copied/tree /dest/path 

If .jpg and .JPG are your only issues, that should just work.

If the problems turn out to be more profound after all, though, it may also be of interest to you that pax supports...

-i

Interactively rename files or archive members. For each archive member matching a pattern operand or each file matching a file operand, pax will prompt to /dev/tty giving the name of the file, its file mode, and its modification time. pax will then read a line from /dev/tty. If this line is blank, the file or archive member is skipped. If this line consists of a single period, the file or archive member is processed with no modification to its name. Otherwise, its name is replaced with the contents of the line. pax will immediately exit with a non-zero exit status if EOF is (CTRL+D) encountered when reading a response or if /dev/tty cannot be opened for reading and writing.