What can I do to make broken link checker not delete my images?

I'm an intern, And I was tasked to make a uploading system which the user can upload images and other kinds of file. I already made the system and it is working fine, The connection to the database works great and everything seems fine, I also publish it at 000webhost. Then, my boss came and told me to copy the url of the website and then paste in broken link checker. No broken links but when I refresh my system all the images are gone, Even in the database. He told me fix this and I have no idea what to do. He also told me that Google does check your website for broken links occasionally and if I don't fix this, The images in the future will be gone. Does anyone know how solve this issue?