This is not a good idea to delete/cut/copy-paste existing nse files while Altiris Services and W3WP service are running.
Better to stop these services, change required core settings and start services back running.
If you are going to change this core setting "DBTimeoutDelayMSecs" then it doesn't require Altiris Services restart (Check documents in this Article where shown which Core Setting changes requires Altiris Services restart or not https://knowledge.broadcom.com/external/article?articleId=180751
Mohamad Sukry Ilias: We often discover not processed NSE. sometime, NSE remains not processed due to problems such as communication with the database .
Igor Perevozchikov: I would suggest to review current core settings and adjust them in mentioned above Articles, comparing of how much CPU, etc current ITMS Server has.
What SMP version you have?
Do you have same default value "400" for "DBMaxPoolSize" core setting?

Did you try to identify which process(s) consuming lot of connections to database and causing nse processing failure?
If you have SMP 8.7.2 or 8.7.3 version, then there is a "Core Performance" Console page available where you can check how many connection are established now in IIS SMP and Database as well as adjust current Event Queue processing core settings

Best regards,
IP.