Flipped Tiles lose Navigation Layer data

### Tested versions

Godot OSX 4.5.beta.5 and 4.4.1

### System information

Godot v4.5.beta5 - macOS Sequoia (15.6.0) - Multi-window, 1 monitor - OpenGL 3 (Compatibility) - Apple M1 Max - Apple M1 Max (10 threads) - 64.00 GiB memory

### Issue description

Tiles with navigation layer data after getting flipped lose that data. This only happens when the tile gets flipped. Rotating the tile preserves the data.

### Steps to reproduce

https://github.com/user-attachments/assets/307f5573-1a62-4a74-b6e8-533cf7ca1a90

Create TileSet, add navigation layer data to it. Add NavigationRegion2D, set the NavigationPolygon Source Geometry Mode to Group With Chlidren. Flip one of the tiles using either shortcut or button on the GUI and add it to the tilemap.

### Minimal reproduction project (MRP)

[bug-report-flipped-tile.zip](https://github.com/user-attachments/files/21798828/bug-report-flipped-tile.zip)

Start with the attached minimal reproduction project and follow the listed steps in the Godot editor to confirm that flipping a tile removes its navigation layer data while rotation preserves it. Trace the tile-flipping path and verify that flipped tiles retain their navigation data without regressing rotation behavior.

Written by the indexing model from the issue text.