The key is:

< 2016-07-19 09:07:14.323 Script: Using configured synchronization options different from factory defaults.
. 2016-07-19 09:07:20.853 Collecting synchronization list for local directory 'E:\YTP-M\DATA\YTP\20 BIM Department\01_WIP\02_NAV\10_NWC\01_STR' and remote directory 'YTP_01_WIP/10_NWC/01_STR', mode = Local, params = 0x1203 (Delete, NoConfirmation, NotByTime, Mirror)

You have configured in GUI not to use timestamp criteria for synchronization.
And you did not isolate the script from the GUI configuration:
https://winscp.net/eng/docs/scripting#configuration

We distribute files and their updates via our FTP server.

The synchronization script is:
synchronize local -mirror -delete "E:\YTP-M\DATA\YTP\20 BIM Department\01_WIP\02_NAV\" YTP_01_WIP

The FTP server is located in UAE.

In all our offices the script works fine, except in the office in UK.
We have ran the script on the server as well as on a PC, and both scenario's gave the same problem:

=> new versions of existing files are not getting downloaded

Please note that new files (in other words, the file does not exist yet on the target) do get downloaded => this is correct and as expected.

I have attached the logfile (copied into an excel file) and indicated in red an example of a file which is not updated on the target.