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Only an additional idea and maybe you did something similar.
I had a problem a couple of weeks ago. What happen? I had a custom column with a bad design. Therefore I decide to change this column. I did it the way that I define a new one with a similar display- and column name and add a digit to it to have it different to the old one. I update then the content to the new column, check the results of the database and was happy that everything was working well. I thought…
After this, I delete the old column and rename the new one to the old column name. So fare so good. Next day Friday, I made a Calibre update and after this, I switch to my test library for testing some other things. Some when later I switched back to my main library because I had to add a book there and I was heavily surprised to wait about 3 (!) minutes for adding a book and then additional 3 minutes for updating my metadata. Doing this with my test library, this process takes only a second.
I check my main library again; I saw that I made a stupid thing:
I renamed my new column display name but I forgot to rename the column name itself. Unfortunately the old column was part of a virtual library and every time I made a change in the metadata, Calibre try to update the data and was not able to do that what result in a long activity to update the caching data (I guess). After I changed the column name to the correct name the library runs like charm again. My lesson learned…
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