A Lotus Open Mic presentation on compact -replica makes clear the -restart option can be used with multiple databases in an *.ind file
http://www-01.ibm.com/support/docview.wss?uid=swg27039379
Entries in log.nsf indicate the ind file and -restart are working. e.g.
06/08/2014 07:15:33 Compacting /home/notes/data/ddm.nsf (Domino Domain Monitor (8)), weekly_compact.ind -REPLICA -RESTART
> drop ddm.nsf
06/08/2014 07:15:40 Compact -REPLICA failure, rename of dirty NSF file, DB: /home/notes/data/ddm.nsf
06/08/2014 07:15:40 Error compacting /home/notes/data/ddm.nsf, weekly_compact.ind -REPLICA -RESTART: Database is currently in use by you or another user
06/08/2014 07:15:40 Database compactor deferring 'restart server' for /home/notes/data/ddm.nsf, weekly_compact.ind -REPLICA -RESTART