Lemmy has built in block support for instances. I would advice you to block instead of muting since it will transfer between apps.
Boost For Lemmy
Community of the Android app Boost for Lemmy
I'm not going to use other apps. When Boost stopped working on Reddit I quit the site. I've used Boost for a long time.
I think you misunderstand. Lemmy is just the back end that instances use. Boost will interact with the lemmy API. What I'm saying is that lemmy already has a way to block communities not tied to boost. So any bugs you have encountered by muting instances with boost, shouldn't be there if you use block instead of mute, since the lemmy backend will do all the work instead of boost.
I could totally be wrong, but I think muting is just the terminology Boost uses for blocking - I had a bunch of sublemmys blocked in Thunder and they were listed as muted already when I first installed Boost
Boost has options for both muting and blocking instances. I know that block utilises lemmy's features as it will sync with blocked communities/users that you do outside of boost.
Mute I'm fairly sure is boost specific as muting won't sync outside of boost, and there is an option to mute instances. Until lemmy 19.0 (currently at 18.x), there isn't a built in way to block instances so that must be something boost does on its own.
Thank you for clarifying!