COPY_ONLY option can be used anytime and the file can be taken away or disappeared without affecting LSN chain. If you take a full backup on-demand without using COPY_ONLY option, you need to keep the file in the same place where it can be found with other backups. There are two tables msdb..backupmediafamily

msdb..backupset

that record how backups were taken (assuming you can recover msdb).

For 3rd party tools, if it breaks after a ad-hoc full backup is taken (quit taking log backup), you need to quit using that crapy tool. SSMS native maintenance plan or T-SQL code do just fine.

If somebody took a backup and the file can not be found, and you are the one need to restore with that file, you are screwed. Update your resume.

With full and diff backups, you can always take an ad-hoc diff backup, follow the same rule above to safe-keep the file.

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COPY_ONLY

Specifies that the backup not affect the normal sequence of backups. A copy-only does not affect the overall backup and restore procedures for the database.

You can create a copy-only backup for any type of backup. The effect of the COPY_ONLY option varies with the general backup type, as follows:

A data backup taken with the COPY_ONLY option cannot be used as a base backup for differential backups. Differential backups taken later will behave as if the copy-only backup does not exist.

A differential backup is unaffected by the COPY_ONLY option.

A log backup taken using the COPY_ONLY option does not truncate the transaction log.