Short answer? Upgrade ![:)]( "Smile")
SyncBackFree has no previous-state history, and thus if a file is on X but not Y, it cannot tell if this is a new file recently added to X or the result of a deletion from Y (because it has no record what was on X or Y last time). You thus have to tell it whether to delete all such files (in this case, from X, but could be either) or to copy all such files (in this case, to Y, but could be either). You can do either action, but obviously you cannot set it to do both actions at once - so you have to pick one...
It's mentioned here (look for the entries mentioning 'Smart Synchronization' (as opposed to 'Basic Synchronization')
Help > Search > 'synchronize' (without the quotes) > hits 2 & 3 have more background (but don't let that prevent you from reading the other hits)
SyncBackSE/Pro have SmartSync, and can generally figure such things out (on run-2 and later: in run-1 they have no History, they're 'building' it right then on that run #1 for use on future runs)
SyncBackFree has no previous-state history, and thus if a file is on X but not Y, it cannot tell if this is a new file recently added to X or the result of a deletion from Y (because it has no record what was on X or Y last time). You thus have to tell it whether to delete all such files (in this case, from X, but could be either) or to copy all such files (in this case, to Y, but could be either). You can do either action, but obviously you cannot set it to do both actions at once - so you have to pick one...
It's mentioned here (look for the entries mentioning 'Smart Synchronization' (as opposed to 'Basic Synchronization')
Help > Search > 'synchronize' (without the quotes) > hits 2 & 3 have more background (but don't let that prevent you from reading the other hits)
SyncBackSE/Pro have SmartSync, and can generally figure such things out (on run-2 and later: in run-1 they have no History, they're 'building' it right then on that run #1 for use on future runs)