This can be done in several ways. Below you see 2 options. They do the same thing only one uses qualifiedByName while the other uses expression. Depending on your need one might fit better then the other.
Using a custom method found by mapstruct
qualifiedByName required because otherwise mapstruct does not know which method to use.
    @Mapping(source = ".", target = "startTime", qualifiedByName = "startTime")
    @Mapping(source = ".", target = "endTime", qualifiedByName = "endTime")
    AvailabilityRuleDTO toAvailabilityRuleDTO(AvailabilityRule availabilityRule, @Context Schedule schedule);
    @Named("startTime")
    protected ZonedDateTime startTime(AvailabilityRule availabilityRule, @Context Schedule schedule) {
        return convertTime(availabilityRule.startEpoch, schedule.timezoneId);
    }
    @Named("endTime")
    protected ZonedDateTime endTime(AvailabilityRule availabilityRule, @Context Schedule schedule) {
        return convertTime(availabilityRule.endEpoch, schedule.timezoneId);
    }
    private ZonedDateTime convertTime(long epoch, String timezoneId) {
        Instant instant = Instant.ofEpochMilli(epoch);
        ZonedDateTime time = LocalDateTime.from(instant).atZone(timezoneId);
        return time;
    }
Using a custom method configured by an expression
@Named used here to prevent mapstruct from accidentally using this method for other mapping actions. Without it it will most likely still work.
    @Mapping(target = "startTime", expression = "java(convertTime(availabilityRule.startEpoch, schedule.timezoneId))" )
    @Mapping(target = "endTime", expression = "java(convertTime(availabilityRule.endEpoch, schedule.timezoneId))" )
    AvailabilityRuleDTO toAvailabilityRuleDTO(AvailabilityRule
                                                availabilityRule, Schedule schedule);
    @Named("time")
    protected ZonedDateTime convertTime(long epoch, String timezoneId) {
        Instant instant = Instant.ofEpochMilli(epoch);
        ZonedDateTime time = LocalDateTime.from(instant).atZone(timezoneId);
        return time;
    }
Complete mapper including schedule
@Mapper
public abstract class ScheduleMapper {
    @Mapping(target = "timezone", source = "timezoneId")
    @Mapping(target = "rules", expression = "java(toAvailabilityRuleDTOs(schedule.getRules(), schedule))")
    abstract ScheduleDTO toScheduleDTO(Schedule schedule);
    @Named("rules")
    abstract List<AvailabilityRuleDTO> toAvailabilityRuleDTOs(List<AvailabilityRule> rules, @Context Schedule schedule);
    @Mapping(target = "startTime", expression = "java(convertTime(availabilityRule.startEpoch, schedule.timezoneId))")
    @Mapping(target = "endTime", expression = "java(convertTime(availabilityRule.endEpoch, schedule.timezoneId))")
    abstract AvailabilityRuleDTO toAvailabilityRuleDTO(AvailabilityRule availabilityRule, @Context Schedule schedule);
    @Named("time")
    protected ZonedDateTime convertTime(long epoch, ZoneId timezoneId) {
        Instant instant = Instant.ofEpochMilli(epoch);
        ZonedDateTime time = LocalDateTime.from(instant).atZone(timezoneId);
        return time;
    }
    String map(ZoneId zoneId) {
        return zoneId == null ? null : zoneId.getId();
    }
}