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Acronis Active Protection permanent disable

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We have been deploying Acronis True Image for a while now and have had multiple issues with the Active Protection causing unexpected "false alerts" for the applications we run. Initially, we were disabling Active Protection Service from the Windows desktop or command line. Our IT management asked that we stop doing this, as they claimed this stops all backup services too. I have not seen that happen and on all machines we checked over the past couple of weeks, the Active Protection is showing disabled, but backups are up to date.
I know there is an article describing how to permanently disable from the desktop using the application itself, or the Systray icon, but some times we need to deploy the disabling action without interrupting the application that is running. Is it OK to use the sc command to perform a permanent disable of APS and will it cause adverse effects to the backup schedule in the long term?

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