How to update, ensuring it doesn't conflict with application repositories?

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Hi,

I have some servers with application repositories, for example:
/etc/yum.repos.d/app1.repo
/etc/yum.repos.d/app2.repo
/etc/yum.repos.d/redhat.repo
What is the best practice for updating OS and ensuring:
- only the active repositories on redhat.repo are used
- ensures that application updates can occur at any time and does not conflict with updates with OS updates.

Thanks in advance
MBrito

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