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I am using a custom CRS for a project and whenever I load a .shp file, QGIS (3.8.2) creates a new custom CRS entry. As of today, I have about 10000 entries that are all the same and would like to delete them. Can I do it all at once? Clicking the minus sign is becoming tedious, since there is about a second of delay between each click.

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Custom crs are stored is a sqlite database table tbl_srs. The database itself is under your profile path and the file is called qgis.db. So, it should be safe to delete the rows of the table. To do that, close QGIS, make a copy of that db-file (if something goes wrong...), and open qgis.db in a sqlite-database sql-monitor, like spatialite-gui or sqlitebrowser. Then you can use a sql expression to delete the rows. For example DELETE FROM tbl_srs removes all entries in the table. Make sure to disconnect your sql-monitor from the database (close it) and start qgis again.

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