It's usually standard operating procedure for files like this to be written to a temporary filename, and then renamed to their final name only after the transfer is completed. This essentially guarantees that the file that's there will always be in its final complete form. If your script opens this file, begins reading from it, and the FTP session suddenly comes in and starts saving its own file, these won't clash. In the event it's finished before you are, by renameing it, it simply unlinks your file and replaces the filename with the new one. Since you still have an open file handle, your data isn't affected. I might note in the control file that this update has been processed prior to you opening the file, just so that in a case like this you can pick up the new change next time.

An alternative might be to use lock files. Have the FTP server send a lock file before it starts uploading, remove it when it's done, and have your script honor it. If you have a great deal of control over the FTP process on the other end, such a lock file could work both ways.