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The Q&A How to cleanly upgrade QGIS on Windows? outlines steps to upgrade QGIS. An important step recommended is "Make copy of plugins directory located here C:\Users\yourUserName\.qgis2\python\plugins and then delete the .qgis2 directory."

Are there not other elements besides the plugins folder to save for the new installation, that would otherwise be removed when uninstalling the version to be replaced? Is there a recommended process for storing such elements in protected locations outside of QGIS install folders?

  • The .qgis2 folder will not be removed by any upgrade, nor is it necessary to delete it manually unless you are running into problems. Regularily saving your self-made processing algs/models and your GIS data (projects and sources) is recommended anyway. – AndreJ Apr 24 '17 at 5:32
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I generally save a copy of the following folders:

  • scripts, which stores the custom scripts (it is located in .qgis2/processing);
  • models, which stores the custom models (it is located in .qgis2/processing);
  • plugins, which stores the installed plugins (it is located in .qgis2/python);
  • expressions, which stores the custom function for the Field Calculator (it is located in .qgis2/python).

As @AndreJ correctly said, the .qgis2 folder is generally not removed when installing a new version but, if you are upgrading from a very old QGIS version, you could encounter some problems using the Processing plugin (problems with QGIS itself or other providers).

So, if you don't want to deal with any problem, I suggest to backup the folders described above and then deleting the .qgis2 folder, since it will be created again after the first start of QGIS.

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