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madeleinelevy - did your 'clean install' necessitate rebuilding your library? I ask because the link from the Book Comment to the image file is stored in the library database and a 'clean install' of calibre does not touch any existing libraries.
If you moved the image folder then you should be able to use the Bulk Metadata Edit Search and Replace feature to 'repair' the HTML - I know this works 'cause I've done it
If you really want to embed the images maybe this will work ==>>
How To Embed Images Directly Into Your HTML
I have NOT tried it in this context, so I don't know if it will work in a calibre Comment.
If you have many images and/or they are large it will increase the size of the database and that may have a deleterious effect on performance. Calibre uses an in-memory 'copy' of the database, I don't know if that includes Comments but if it does then you may run into 'out of memory' problems.
Probably best to wait for a response from Kovid and/or chaley before you commit to this path.
BR