If the files uploaded by another tool has different naming convention with the new ones, you could use option /Pattern to upload only the new files,
e.g. old files have naming convention like “abcxxxx”, new files have naming convention like “xyzxxx”, then please specify /Pattern:xyz* to copy the new files only.
Or use option /xo (means exclude old files) to copy new files only, note that AzCopy will compare local files' change time with the 'Last Modified Time' of the destination blobs when you specified option /xo and /xn, please make sure the uploaded old files’ ‘Last modified time’ is same or newer than the their local copies’ change time, otherwise the old files will be uploaded again when you specified option /xo. You can use option /MT to set ‘Last Modified Time’ as same as local copies’ change time during upload.
For more details, please visit http://aka.ms/azcopy
Thanks