" What would I do differently?" The last thing I would have done is fill it in. I would have inspected in hopes of finding how and where it was supposed to drain. Failing to find and clear drain I would have called a contractor authorized by mfgr to install and repair whatever material is on roof. Is it EPDM or torch-down?

I've overseen several buildings with flat roofs and if I was able to find them always used original installer for any and everything that was required. On the rare occasions where original installer wasn't available I used another manufacture authorized contractor. Flat roofs are not diy.

At this point pray you didn't cause a problem that is expensive to remedy.

Again, you have had 15 years of water infiltration into your home. Now you bring up this issues. Again keep them all to one post as they are all issues that "could" be the source of your water issues. An NO you do not take roof coating pile it on to fix ponding issues. One of the worst things you can do.

You can always wait until it rains and go take a look.