Ok so in the input filter you need to use set bgp-path-peer-prepend or else it does nothing...
(in v6 set-bgp-prepend=3 worked both in input and output filter)
It looks like the conversion from v6 to v7 handles this incorrectly. Problem is of course that a filter cannot know if it is input or output filter, and in v6 it could be both.
Well, the filter conversion has more problems than that. E.g. it forgets to append an "accept" entry at the end of each chain, which is there implicitly in v6.
Maybe you could issue some warning to upgraders that they need to manually review their filter rules after upgrade, and what to look for.
(in fact I would appreciate it when you displayed a warning pointing to some page on help.mikrotik.com when users try to do a v6 to v7 upgrade and where you explain any known issues at that time, and that e.g. BGP is a work in progress so users that use BGP should be extra careful and/or ask their peers first)