Filebeat not detecting all changes made to csv File

This might explain why you are getting partial lines as well. If a line earlier in the file all of a sudden increases in size, it is possible a partial line could be read as Filebeat uses the file offset to keep track of what has been processed.

Filebeat is not designed to handle this scenario, so I do not believe that is possible.

I think the altering of prior content may be at fault here rather than the method with which the file is copied.