Overview Creation fails in geopackages created using Tiling Scheme

[Augustus]

The following command will cause a crash for large tiled images. With small tiled images the overviews creation is done fine

gdal_translate -of GPKG byteError.tif gpkg.gpkg -co TILING_SCHEME=GoogleMapsCompatible
gdaladdo gpkg.gpkg 2 4 8 16 32

You can reproduce this issue by re-sampling the byte.tif to 9999 rows and columns and then manipulating the resultant tif file using the above commands ​https://github.com/OSGeo/gdal/blob/trunk/autotest/gdrivers/data/byte.tif I have attached the intermediate files.

Update: Workflow for reproducing the issue

[Even Rouault]

I guess this is the same as #6335 I cannot reproduce any issue after the fixes done in #6335 (instead of the error message you got in #6335, crash was also likely)

[Augustus]

I was able to reproduce this issue with larger images. Steps to reproduce this issue

Data is Attached byte4800.tif

gdal_translate -outsize 9999 10118 byte4800.tif byteError.tif
gdal_translate -of GPKG byteError.tif Test.gpkg -co TILING_SCHEME=GoogleMapsCompatible

Error

ERROR 1: sqlite3_exec(UPDATE partial_tiles SET zoom_level = -21, partial_flag =
0 WHERE zoom_level = 20 AND partial_flag != 0) failed: columns zoom_level, tile_
column, tile_row are not unique
ERROR 1: sqlite3_exec(UPDATE partial_tiles SET zoom_level = -21, partial_flag =
0 WHERE zoom_level = 20 AND partial_flag != 0) failed: database disk image is ma
lformed