How to remove the backgrounds on a placed image on InDesign?

Hi all, I have an InDesign file that I created a couple of years and a computer ago. I created several different flower designs in Illustrator, then placed them on the flyer I was designing. I cannot find the AI files anymore, leaving me with a lot of linked errors. The document looks fine when I made changes and checked it in the Presentation mode, but when I saved it to pdf (print) all the AI files have a white background when originally it was transparent. Is there a way to remove this? I really don't want to have to redesign a bunch of different flowers.

When saving the pdf, I did try to save it in Adobe 4 with the Transparency Flattener to High Resolution (found this suggestion). It didn't change anything. Thanks for your help.