Loaded and re-saved in QGIS c53d416c with Qt 6.7.0 (Windows, Virtualbox) #6
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Using the windows executable from https://github.com/qgis/QGIS/actions/runs/9731000236 of qgis/QGIS#57414 The .lyr file was not "loaded" per se, but used and with the loaded layer then a new .lyr was exported.
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Resaved the files in another test build of QGIS with Qt6: The attributes are in the same order as in my Qt6 build.
The other differences are not related to this "investigation".
Using the windows executable from
https://github.com/qgis/QGIS/actions/runs/9731000236 of qgis/QGIS#57414 on Windows with Virtualbox
Libraries
QGIS version | 3.39.0-Master
QGIS code revision | c53d416c
Qt version | 6.7.0
Python version | 3.11.9
GDAL/OGR version | 3.8.4
PROJ version | 9.4.0
EPSG Registry database version | ()
GEOS version | 3.11.3-CAPI-1.17.3
SQLite version | 3.45.3
PDAL version | 2.5.3
PostgreSQL client version | unknown
SpatiaLite version | 5.1.0
QWT version | 6.3.0
QScintilla2 version | 2.14.1
OS version | Windows 10 Version 21H2
Active Python plugins
db_manager | 0.1.20