I am using Cobian Backup. I want to keep a partition in an internal drive in sync with another partition in an external drive.
What should I choose? Incremental or Differential?
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Since you only want to have your partition synched, I recommend to use the incremental option, but also having the "create separated backup using timestamps" option turned OFF. That is found under the task properties, in "general". That way, you will only copy new and modified files without having to deal with different versions or separated backups.
Also, even if you already have some of the files in the target partition, the first time Cobian makes a backup, by default it will try to make a FULL backup (despite setting it to incremental) and it will in fact overwrite files because it being the "first time" backup. To avoid that, go to Options > Engine, and be sure to turn off "First backup always full". That is always recommended if you are just "updating" a previous backup made from just copying files manually.
Another thing, if you manually copy files after a backup to the new partition, and you don't want to "waste time" copying (in fact overwriting) them because Cobian thinks they've been copied from the source, be sure to turn off the "use file attribute logic" option OFF, under General options in the task properties. That is because by default, Cobian "knows" that a file is backed up by an attribute called "archived", and not by seeing the file itself already there. Since you only want to copy new and updated files, and you probably already have some files there, turning off that option means that it will not re-copy files that are already there (unless they are newer).
Since you are not creating separated backups, every time you backup, you will only have ONE backup version of everything, besides you will not have additional folders with several dates and versions of some files, which is what you want. That is, you will have a copy of the same files and folders structure from your source partition.
With that settings, the backup will actually only make a copy of new and modified files from the source partition into the target partition, but it will NOT delete files from the target partition if you delete them from the source one.
If you DO want to have an exact copy of A into B, meaning you will also delete files from the target if you delete them from the source, you then would need to also turn on the option "Mirror Task", under Advanced, in the same task properties dialog.
Additional notes: some other backup programs by default create more folders when creating backups, e.g. D:\someFolderCreatedByBackupSW[..someDate..]myActualData[...] instead of just: D:\myActualData[...]
Even if those folders contain your data, they don't "respect" the exact same top level folder structure you have, besides, if you want to restore such backups, you still need the same backup program to get everything back (Areca works that way, afaik).
You also may want to keep compression and encryption OFF by default, because otherwise, the files will not be available directly from outside Cobian or without having to uncompress them. With that off, you always have the last data, as an exact copy of the source, and readable just as any other media.
Hope that helps! Be sure to ask further if I gave you more doubts =P