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Changes to the ignore patterns are detected before each scan or sync operation.
Syncthing never deletes anything that is added to an ignore file, if it’s already there it’s there and you’ll need to delete it manually after ignoring. (Or leaving it un-ignored, deleting it somewhere and letting that sync, and then deleting it.)...

Okay, background on the rename detection mechanism:
Syncthing scans for changes. The filesystem notifications we get (when enabled) triggers the scanner.
The scanner traverses the thing it was told about. Sometimes this is a single file, sometimes it’s a parent directory, sometimes it’s the entire folder. Notification events are aggregated so if we see more than a threshold of events in a given directory...

The point is Syncthing is likely unaware of the MFT change and would likely scan the new file and could only detect that the hash was the same to assume it was actually a rename or move.

Admittedly, I was assuming that Syncthing was paying attention to the files themselves more than their filenames for this purpose.
In other words — and I do not claim to be expert on any filesystem — renaming a file or directory should result in the MFT being appropriately updated but not any bit of the file being changed....