It is possible by dumping, editing and reimporting the table.
This script will do it for you (Adapt the values at the start of the script to your needs):
#!/bin/bash
DB=/tmp/synapse/homeserver.db
TABLE="public_room_list_stream"
FIELD=visibility
OLD="BOOLEAN NOT NULL"
NEW="INTEGER NOT NULL"
TMP=/tmp/sqlite_$TABLE.sql
echo "### create dump"
echo ".dump '$TABLE'" | sqlite3 "$DB" >$TMP
echo "### editing the create statement"
sed -i "s|$FIELD $OLD|$FIELD $NEW|g" $TMP
read -rsp $'Press any key to continue deleting and recreating the table $TABLE ...\n' -n1 key
echo "### rename the original to '$TABLE"_backup"'"
sqlite3 "$DB" "PRAGMA busy_timeout=20000; ALTER TABLE '$TABLE' RENAME TO '$TABLE"_backup"'"
echo "### delete the old indexes"
for idx in $(echo "SELECT name FROM sqlite_master WHERE type == 'index' AND tbl_name LIKE '$TABLE""%';" | sqlite3 $DB); do
echo "DROP INDEX '$idx';" | sqlite3 $DB
done
echo "### reinserting the edited table"
cat $TMP | sqlite3 $DB