Some 64bit plugins also have a different filename than their 32bit version. If you have only the 64bit one installed but not the 32bit one, then Renoise will report a missing plugin for those cases. Renoise doesn’t care for the actual plugin ID but uses the filename instead to identify a plugin. If you happen to run into such problem, then you can use a small script i have written to update the plugin filename inside the song and fix it.
https://forum.renoise.com/t/snippet-replace-plugin-ids-inside-song-xml/35228