For ftp, no
For ftp over vpn (FTPS), yes
Check your ftp.config file to see if it's specified a particular key repository to look in. As far as ssh, as long as your config isn't specifying an different repository, it should work.
Here's a test. Try to ssh into a remote location (google offers a free mini-cloud accounts but their a little tricky to ssh into). If you can ssh with your certificates in the default location, than the failure of ftps is probably being caused by that services configuration options.