I think that what you describe is the same or at least similar to the issue I have been experiencing.
I prefer to use the Ancestry website to review hints and to attach facts and sources to those in my tree on the Ancestry website as this also enables me to separately download source documents and store them in individual files on my computer. I then use TreeShare to update my RM file.
Yesterday, after entering a few bits of information into RM, I needed to upload my tree to Ancestry again. Shortly after doing so, like you, I started getting the Ancestry hints again. I also thought that these were redundant given that the vast majority of my sources had come from Ancestry in the first place. However, I decided to look at some of my ancestors' profiles on the website and discovered that the sources uploaded from RM, despite originally being from Ancestry, were shown on the site under "Other Sources" rather than under "Ancestry Sources". I imagine that Ancestry hints depend on what, if anything, appears under "Ancestry Sources".
I am not sure whether this is something that Development can fix or whether it is for Ancestry to deal with. Either way, I would hope that something can be done to get the Ancestry website to correctly recognise its own sources even if they do come from other programmes such as RM.