Hi Damir,
thanks for following up. I have confirmed your worfklow as in installing and deploying an OMERO 5.2.1 server locally, importing the image linked above, confirming the initial exception and upgrading the server to OMERO 5.2.2 and receiving the same INFO in the logs as you do.
In order to regenerate the pyramid for the old images, you will need to remove the existing dangling pyramid files for these images. The best way to do this via the API is to use the omero.cms.ManageImageBinaries command against the image ID while setting deletePyramid to true. An example of usage of this command is in the CLI FS plugin. You should be able to write either Python script (or a CLI plugin) to use it against a set of images. Once the pyramid is deleted, a new pyramid should be regenerated when requested e.g. via the OMERO.web interface.
Let me know if this approach successful and I will amend the documentation to mention this command.
Sebastien
