I think I finally found why deleting broken transform stopped working, and probably this fix the @hvelarde issue too, and every other issue similar to this ones.
Sometimes I really like the idea to find a DeLorean, go back in time at the moment when we started adding persistent utility and using the component registry and say "I'm a time traveller that came from a dark future. Don't do this, is a bad idea".
So, I found I was not able to create new Poi issues due to
ValueError: Unknown mime type text/x-web-intelligent.
I found that the mimetype_registry I have was a lot different than on from a whole new site + Poi.
One time again: deleted the tool from my site and copied one from a test site.
After some debugging I found that:
... but ...
mtr = getToolByName(context, 'mimetypes_registry')
Now is easy to get why. We have a persistent utility that is someway different from the tool object (probably because those tools implements a cache? I don't know).
Fix this is easy: just rerun the "Local Component Registry" import step of Products.MimeTypesRegistry.
After this I was pretty sure that portal_transforms tool was hit by the same issue.
After a rerun of Local Component Registry of Products.PortalTransforms my startup warnings disappeared, I can create Poi issues and the Sun is shining in the sky.