You will need to look through the help file to determine exactly how the sync rules and conventions for whatever software you are using operate. There might be options to change the behavior.
The general consensus of sync programs is to make one directory look like another. If something is deleted “here”, it is usually deleted “there”.
Sync programs can be set to examine and entire disk, a few folders, or just a few files. They can also maintain multiple time-stamped copies of the same data as the backup ages and matures.
You may need to perhaps run some test scenarios to be fully confident of what transpires during a backup. As I just got through saying in another post I just made:
"The most important thing with backups is to know exactly what is getting backed up and what is not. A backup program should be clear and concise with no ambiguity as to what is happening.
Personally I use a simple strategy of imaging the main disk from time to time. This captures everything in one fell swoop. And I can restore my system immediately at a moment’s notice. When I’m working with important files I’ll save two copies periodically.
The point here is to have two copies of everything. And to also know you can restore the system successfully. This means that you’ll have already tested the solution and have complete confidence it will work as intended."
I won’t pretend to know the specifics of what you are using, or the details of your setup. I will take a guess and say the answer to your question is YES! Especially if it’s a mirror-type of operation. Each backup program is subtly different and has different options. You may be able to change settings that will affect this behavior. Why not conduct a test? But do so only after you know you have two copies of the data you’re working with. This may mean borrowing a third drive temporarily to hold a backup that you know functions correctly.