It is the difference in time that rclone will use as a basis to compare files to say if a file has been updated. For example, if a file on your local host had a time difference of less than 1 ms between the source and destination, it would think that file is new.
This is most useful when a remote or a file system doesn’t keep the same accuracy of time recordings.
--modify-window duration Max time diff to be considered the same (default 1ns)
Different filesystems may store times to a different level of accuracy. For example, FAT only keeps time stamps to a 2 second accuracy. That means a file timestamped 11:48:15 on your local machine may show up as 11:48:14 on FAT.
Tools that sync between servers with different file systems need to keep things like this in mind; who knows what timestamp granularity is present on the remote server (or even if the clock is in sync properly)?
So if two files (one local, one remote) have a timestamp that is within the “modify window” then the times are considered the same, otherwise the code may end up resyncing the same file every time.
The default is small enough that this function is effectively disabled.