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Sync API deleting assets from server

Hi All,
We have been using Contentful CMS for few years now and had no issues but recently we are experiencing some issues while using the Sync API with JavaScript. I have integrated the Sync API with Javascript onto our web app and use it to save files from the ctfassests location to our own server from where it fetches the files (pdf’s and images) but recently when we update and content block or media and use the sync feature it actually deletes some old files from our server (not the ctfassets).
I then have to manually upload these files onto our server via ftp and it all works fine. its just when we again sync the same files get deleted. I have deleted those entries from cms and recreated them and still have the same issue. Not sure if this a known issue or has any config been changed in the sync api which I would need to implement. any help is appreciated