Sorry, the last part didn't make it right to the list, so here we go
again:

> to remove specific files:
> 
> swish-e -r -i filetoremove -f index.idx -c swish-e.config

This also doesn't seem to work. Or am I doing something wrong?

Search for the word "demohu", it's found:
swish-e -f index.idx -w"demohu*"
# SWISH format: 2.5.2
# Search words: demohu*
# Removed stopwords: 
# Number of hits: 1
# Search time: 0.004 seconds
# Run time: 0.009 seconds
1000 /attachments/SM/XM08.doc "XM08.doc" 19456

Try to remove that file from the index:
swish-e -r -i /attachments/SM/XM08.doc -f index.idx -c swish-e.config 
Indexing Data Source: "File-System"
Indexing "/attachments/SM/XM08.doc"

Checking file "/attachments/SM/XM08.doc"...
  XM08.doc - Using TXT parser -  (9 words)

Removing very common words...
no words removed.
Writing main index...
Sorting words ...
Sorting 9 words alphabetically
Writing header ...
Writing index entries ...
  Writing word text: Complete
9 unique words indexed.
4 properties sorted.                                              
1 file indexed.  74 total bytes.  9 total words.
Elapsed time: 00:00:00 CPU time: 00:00:00
Indexing done!

Search again, it's still found:
swish-e -f index.idx -w"demohu*"
# SWISH format: 2.5.2
# Search words: demohu*
# Removed stopwords: 
# Number of hits: 1
# Search time: 0.001 seconds
# Run time: 0.005 seconds
1000 /attachments/SM/XM08.doc "XM08.doc" 19456