How to make EMCopy 4.16 Copy Locked files?

Answers with reference to your question numbering:

1.a) If your EMCopy command contains the '/c' option, EMCopy will continue after any error (after retries) with the remaining files. If you leave out the '/c' it will not continue, but stop on the first (unrecoverable after retries) error. In other words, whether it stops or continues on an error is entirely up to whoever wrote the EMCopy command line. You mentioned reading that it stopped; possibly what you read did not mention the 'continue' option.

1.b) If a file is locked on the source, it cannot be copied to the target, so EMCopy leaves any previously-copied version on the target alone. EMCopy will only overwrite on the target if the file can be copied. You mentioned reading something to the contrary; possibly what you read is incomplete or incorrect.

2.) Normally, with EMCopy (and Robocopy, and many similar tools) you run several passes. One full copy and several incremental synchronizing passes. Then take down user/application access to the source, do one final pass while no-one is using the source so that everything is fully synchronized, and then cut over to the target system. Some of the more sophisticated migration tools (Data Dynamics "StorageX", Data Dobi "Dobi Miner") have built-in job sequencing for automating these sort of functions. On free tools like EMCopy and Robocopy you just have to remember to do it manually.

Always remember that you can have (due to system, user, or application crashes and other problems in the past) corrupt files, or corrupt directory entries, on the source; making it impossible for those files to be migrated, no matter what the tool. Demanding "no exceptions" on a migration is often an unrealistic goal; going for "only known and accepted exceptions" is more realistic.