So to answer your question: when I upgraded to High Sierra and APFS on one partition, it didn't erase the other partition. Also the same thing happened when I tried booting from my clone of Mavericks.
Same problem continued: the Sierra side would boot, but the Mavericks side wouldn't. Then I tried booting off a Sierra backup, reformatting the whole drive, and restoring both partitions from my clone backups. It gave me a gray apple and then put text over it, including the line "Unable to find driver for this platform: \"ACPI\". It copied okay, but wouldn't boot from that partition any longer.
Problem came when I tried erasing the second partition and restoring my disk image of Mavericks via SuperDuper. I'm pretty sure it didn't, because duplicating large files took some time, which is supposed to be eliminated in APFS. I could still boot off of Sierra in the first portion, and I tested to make sure it hadn't switched to the new file system on that partition. It didn't, but otherwise things seemed to be working. I wanted to see if Adobe CS4 worked with the upgrade. What I tried was this: I upgraded the Mavericks drive (the second partition, I believe) to APFS. That way I can choose which system to boot (mainly because HandBrake works better with Mavericks). I have the drive partitioned into two: my main partition has Sierra, and the alternate has Mavericks. I have a MBP mid-2012, upgraded to 8GB RAM and with a fairly new Crucial SSD (525GB). I'm not an expert, so bear with me, but I tried something similar to what you're describing.
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