Base folders mean what you have specified in your profile as Left & Right (or Source and Destination, whatever).
The issue isn't about new folders 'inside' (deeper than) those base folders, it's about whether or not those pre-specified folders in those strings exist or not.
The issue with the auto-creation of base folders for SmartSync is best described with an example: Ordinarily you can type in a folder in Source or Destination, and SE/Pro will create it for you if it doesn't already exist (saves needing to go and create your Destination folder manually first, for example). Let's say you set up a SmartSync with the following for Left & Right
L X:\Pictures\
R Y:\Pictures\
and let's say you say 'no' to that 'turn it off' question (or, that it didn't exist).
Only Left (X:) has files so far (let's say '27000'). So far so good - run-1 will copy them all to Y.
Now let's say you (or someone else...) thinks the folder on Y: would be better called \Photos\, and changes the name...
Next run, SE/Pro finds there is no folder called \Pictures\ on Y, so it creates it automatically. (Obviously, it will be empty). Then the comparison stage runs, and it finds that out. But it has a database which tells it that last time, Y:\Pictures\ contained 27000 files, but now there are none. So 'obviously' these have been deleted, so it replicates the apparent deletions to X:\Pictures\ - exactly as a SmartSync is set up to do. Cue upset user...
Something similar can happen without anyone changing the name of one side or the other - imagine Windows spontaneously changed drive letters around (which can happen), or you have the usual USB drive disconnected, and something else inserted, that also has the example drive letter Y. When the profile runs, it will almost certainly find that device has no folder called \Pictures\ either, and will create one (that is empty....the rest is 'as above')
Thus, auto-creating a base folder that doesn't exist in these (or similar) circumstances is contra-indicated, which is why a SmartSync will offer to turn that option off for you.
The issue isn't about new folders 'inside' (deeper than) those base folders, it's about whether or not those pre-specified folders in those strings exist or not.
The issue with the auto-creation of base folders for SmartSync is best described with an example: Ordinarily you can type in a folder in Source or Destination, and SE/Pro will create it for you if it doesn't already exist (saves needing to go and create your Destination folder manually first, for example). Let's say you set up a SmartSync with the following for Left & Right
L X:\Pictures\
R Y:\Pictures\
and let's say you say 'no' to that 'turn it off' question (or, that it didn't exist).
Only Left (X:) has files so far (let's say '27000'). So far so good - run-1 will copy them all to Y.
Now let's say you (or someone else...) thinks the folder on Y: would be better called \Photos\, and changes the name...
Next run, SE/Pro finds there is no folder called \Pictures\ on Y, so it creates it automatically. (Obviously, it will be empty). Then the comparison stage runs, and it finds that out. But it has a database which tells it that last time, Y:\Pictures\ contained 27000 files, but now there are none. So 'obviously' these have been deleted, so it replicates the apparent deletions to X:\Pictures\ - exactly as a SmartSync is set up to do. Cue upset user...
Something similar can happen without anyone changing the name of one side or the other - imagine Windows spontaneously changed drive letters around (which can happen), or you have the usual USB drive disconnected, and something else inserted, that also has the example drive letter Y. When the profile runs, it will almost certainly find that device has no folder called \Pictures\ either, and will create one (that is empty....the rest is 'as above')
Thus, auto-creating a base folder that doesn't exist in these (or similar) circumstances is contra-indicated, which is why a SmartSync will offer to turn that option off for you.