Multiple Base Folder Warning

[sbdari]

Hello. I've been using FFS since 2010 and simply love it.
It's has been a major component of my backup and sync strategy, which I've tweaked over the years.
With my latest strategy, (for sake of simplicity in explaining my problem) I've setup two folder pairs.

FIRST FOLDER PAIR: I'm mirror-syncing my computer folder D:\Archives (left) with my external drive E:\Archives (right). I've been doing this for many years and everything works well. The folder 'Archives' contains many folders, sub-folders and files.

SECOND FOLDER PAIR: I started to two-way sync one of my computer folders with OneDrive cloud folder on my computer. It's setup as a D:\Archives\Financial Records\Ratnam Expense Book (left) with D:\OneDrive\Archives\Financial Records\Ratnam Expense Book (right).

Two problems crop up with this setup:
1. When I try to sync, I get a warning (attached) saying "Some files will be synchronized as part of multiple base folders. To avoid conflicts, setup exclude filters so that each updated file is considered by only one base folder".

The trouble is I don't want to exclude anything from the FIRST FOLDER PAIR as that acts as a full backup of 'Archives'.
I don't know what to exclude from the SECOND FOLDER PAIR. In it's Local Filter Settings, I did include this: \Financial Records\Ratnam Expense Book\* but the warning still came. If I ignore the warning (attached) it does sync. My questions is, am I doing something wrong OR should I ignore the warning? I think I'm missing something, hence, doing something wrong.

2. Second problem is that after I ignore the warning, changes in the second folder pair sync alright, but those changes are not picked up by the FIRST FOLDER PAIR. I have to run FFS again, then those changes are picked up and synced by the FIRST FOLDER PAIR. I thought moving the first folder pair below the second folder pair will solve it but it did not. What can I do here?

[Plerry]

If you want the Mirror sync to base folder E:\Archives to include everything from D:\Archives, including D:\Archives\Financial Records\Ratnam Expense Book, you should obviously not exclude anything.
This means there is an overlap with the second folder pair, so the warning is correct.
But, it is a warning , not an error. And with the sync as described, there does not seem to be anything "dangerous" related to this overlap.
The only limitation is as you describe under your item 2): the Compare action compares the left and right locations with their status prior to the sync. So, any changes to the overlap in location as a result of the sync are not part of the comparison and thus do not result in 2nd level actions.

The way to solve this, is by running a second Compare and Sync after the first one (as you describe), or by running two separate FFS syncs in sequence; first the Two-way sync for the second pair (which may results in changes in D:\Archives\Financial Records\Ratnam Expense Book) and then the Mirror sync for the first pair.
You can do this yourself from the FFS GUI, or by sequentially running the two separate FFS syncs from a *.bat or *.cmd script.

[sbdari]

Thank you @Plerry for your detailed response. It's comforting, and reassuring to know one was headed in the right direction. I was fiddling with the notion of running two instances of FFS, but for some reason, it didn't come together...till now. And running a .bat script is also brilliant. Simple and effective. Don't know how I missed that too. Slow week I suppose.

@Zenju I want to express my appreciation for this small, flexible & powerful little application. It is rare a program can be all three. Thank you.