I know David recently updated the categorization of filters and it may have an issue with older versions of G'MIC. I would highly recommend you update to 1.5.6. I too use 64-bit GIMP and do not have any apparent issues with this update. Besides, with the current version, you get Packed Sprites.

Yup some pretty nice stuff in the more recent versions
The filter update method itself was changed sometime around 1.5.5 and works better, but the old versions should still update so long as the authors keep their files hosted.

It's very strange that the filters disappear each time your run a new filter.
When updating, local files containing the new filters are created and stored on your computer, so once it is downloaded, it should be there forever
I don't understand why it doesn't work like this.

The error message you get is not really an issue : it only means one of the filter source cannot be reached, which means only the filters defined in this source won't be available.

when you mark a filter in favorite they are not updated normally.
and G'MIC just leaves them, and once they are updated at G'MIC
the settings are changed and not updated cause are marked as favorites.
At least this has been my experience. Try again after you remove all filters
from faves .

yes because the favs file can't be automatically updated as the filters , and changes in the filters may break old fav

But if happens to some preset you really like , just post the presets, fixing is simple ...

Well simple if you have no hundreds of presets to update ( I DO ! ) ...but if a few i may help