Obviously file will replaced and Qlikview won't warn you.
a scenario here and I have tested it as well.
(1) Task started at 10 AM for ABC.QVW and it takes 15 minutes to complete
(2) You replaced the ABC.QVW with latest version of ABC.QVW at 10.05 Am.
(3) But QEMC save ABC.QVW (earlier version which it picked up at 10 AM) after task execution completed at 10.15 AM.
Thant means you lost your latest version of the ABC.QVW will be replaced by earlier version.
Finally you will have earlier version of ABC.QVW only.
Your developers should check if a reload task is running for a document they will update, and either wait for the job to finish or abort the reload before they save the updated copy of the app to the server.
If the reload is running frequently, they may need to disable the task whilst the new version is saved.
When they have saved the updated app, the reload task can be re-enabled.
If they update an app whilst a reload is running, the completion of the reload will overwrite the document with the original version plus new any data.
Changes to charts, load script etc. saved whilst the reload was in progress will be overwritten.