Yes you can. But you need to make sure that you are not using the external staging option, as in that case the server refers the file from the location you use. I would suggest instead of deleting the file you should rename the file and validate whether things are fine.
Deleting the war after deploy will only work if you are selecting "stage" mode where admin server takes responsibility to copy the deliverables in managed server location. This will fail for both "no-stage" and "external-stage" mode where user need to copy files to location specified during deployment.