I seem to recall there was a thread on the forum about this not too long ago.
The simplest would be to dump one file, using the tools sqlite3, then import into the other, again using sqlite3. Something like (NOT TESTED):
echo ".dump archive" | sqlite3 file1.sdb | grep -v 'CREATE TABLE' >file1.sql
sqlite3 file2.sdb < file1.sql
where file1.sdb is the sqlite database you want to add to file2.sdb.
The first line dumps file1.sdb, removing the 'CREATE TABLE' statement (you don't want it because you already have the table in file2.sdb). It saves the results to file1.sql, which will be full of SQL "INSERT" statements.
The second line then uses that file to insert the new data into file2.sdb.
Needless to say, make backups first.
-tk