I think this is a complicated question with a lot of "it depends" clauses in the answer. You say your first step was to Import the photos into an LR/Cloudy app on your iPad. So, they would have a file name (which you may not see) and other metadata such as capture date, pixel dimensions, etc. And then somehow copies of these images found their way to your Windows computer through some unspecifed path and you imported them into LrC.
So, first thing to understand is if anything in that path to Windows caused anything on the images to change such as file name, capture date/time, pixel dimensions, etc. The more things that got changed in the process, the less likely it is that LrC will detect that they are the same image. So, let's assume nothing changed.
So, if you turn on Sync in LrC, LrC will try to copy those images (full image file) from Lr/Cloud to Lr/Classic. In general this can be thought of as doing an Import from LR/Cloud using the "Copy" mode to a default folder on your Windows machine. As such, I would assume that the standard "don't import suspected duplicates" would take affect and those duplicate images would be skipped. However - this is speculation on my part as I have not tried this.
But, there are 3 things LrC could wind up doing. 1) skip the dups, 2) import the dups, 3) detect that they are dups and sync changes between what's in LR/Classic and LR/Cloud.
Here's what I would do. Assuming that you believe there are some images in LR/Cloud that you have not copied to LR/Classic, I'd copy ALL the images known to LR/Cloud to your Windows machine using whatever method you did before. I'd then import them into LR/Classic and let the "Detect Duplicates" feature weed out the dups. Now you know that 100% of the images in LR/Cloud are also in LR/Classic. I'd then remove all the images from LR/Cloud using one of the LR/Cloud apps such as the Windows Desktop LR/Cloud app. Once that is done, go into LR/Classic and assure that no collections are marked to sync and that your "all synced photographs" special collection in the Catalog panel is empty. Then turn cloud sync on.
At this point nothing should happen as there are no images in LR/Cloud to sync to Classic, and no collections in LR/Classic marked to sync to the Cloud. Now, any new images you put into LR/Cloudy will automatically come down to LR/Classic (full image). If you want images in LR/Classic to go up to LR/Cloud, put them in one or more collections that are marked to sync (this copies Smart Previews - a special kind of reduced pixel DNG -- to the cloud rather than full files).
Maybe someone else has some other ideas or knowledge but as this message wasn't answered for a day, I thought I'd give it a shot even though my expertise in this area may not be as well developed as others on this forum.