I think it is logical that BATWING takes place before JLI, as it is clear that significant time (days? weeks?) has passed between JLI 11 and 12.
For the record, both the JLI cross-over and Batwing's departure seemed forced. I expect BW was removed from the team due to his on-going series and since the JLI (in whatever form it takes) will likely be relegated to guest appearances or a specific story-line, it could raise continuity problems regarding his location and story (i.e. the JLI is last seen travelling through space or time...). That's one reason I have hopes for this team's future after the JLI Annual. It would be kinda hard to have Batwing with the team on Thanagar (for instance) AND in his own series in Africa. Otherwise, why go to the trouble of specifically removing him from a team that will no longer have any real bearing in, or effect on, the DC Universe?
I guess we'll find out in a few weeks, when the JLI Annual hits the stands...