The error,
DEBUG> Filer 'org.apache.xindice.core.filer.BTreeFiler' not available
was caused because linux has a default maximum of 1024 open files. Seems like the more collections and indexers you have, the more open files.
I solved the problem by setting the value for open files higher. this can be done (on linux) by the command.
#ulimit -n 5000
don't know yet what the downside on other processes or system-load is, or could be.