If you mean two
partitions (volumes) on the same physical drive there will only be one Recovery Drive and when you install Sierra that will be a Sierra Recovery Drive, so your dual recovery would be severely compromised. If those partitions (volumes) are on separate physical drives, I would verify..
- if there is a Recovery Drive (RD) on each drive?
- what is the OS version of the RD on each drive and does it match the OS version installed on that drive?
- can you actually boot the RD on each drive?
How do you intend to "Archive" the El Capitan
partition and would that include the El Capitan RD?
I am putting all this emphasis on the RD because I have found it to be highly valuable in recovering three different Macs whose boot volumes had been damaged in one way or another. Without their RDs these Macs would have been very difficult to restore without losing all their data. (The user's in all three cases either had no backup or their backups were unusable for one reason or another.)
The surest way of doing what you propose would be to have Sierra and El Capitan on separate disk drives and personally I would put the "Archived" El Capitan on its own external drive and disconnect it from the system unless It was in use. I have actually done that using an
OWC Envoy Pro mini USB 3 SSD and it worked quite well. I never had a need to recover from it, but I can boot and run from both the RD and the boot volume on the drive. Rotating rust would have been cheaper, but the SSD is noticeably faster and is basically an oversized thumb drive so it is very portable.
