Synchronization has a "mirror" mode, that does what you need:
https://winscp.net/eng/docs/task_synchronize_full#mode

In scripting you enable it using -mirror switch:
https://winscp.net/eng/docs/scriptcommand_synchronize#mirror

We are using the "synchronize remote -delete" command to synchronize various folders and delete files on the target when they are removed from the source.

Sometimes files are manipulated on the target site which results new timestamps and not transfered files because the target files are newer.

Is there a way of forcing the sync to completely ignore the timestamps and do the job nonetheless?

Currently we use a put command before the synchronize command to make sure all the files from the source are transfered. The synchronize command is solely used to delete files on the target when they are removed from the source.