Fixing "a sealed resource is missing or invalid" warning
Ok, I managed to do this. It's dirty but pretty safe so far.

The database holding that info is located under /var/db/DetachedSignatures. This is an SQLite database, so it can be easily modified using the built-in sqlite3 tool. Here's an example session that deletes entries matching the "eclipse" keyword:

# we're using sudo, so be careful
$ sudo sqlite /var/db/DetachedSignatures

# what tables does it contain?
sqlite&gt; .tables
code global

# what are the column definitions in code?
sqlite&gt; .schema code
CREATE TABLE code ( 
        id integer primary key on conflict replace autoincrement not null, 
        global integer null references global (id), 
        identifier text not null, 
        architecture integer, 
        identification blob not null unique on conflict replace, 
        signature blob not null, 
        created text default current_timestamp 
    );
CREATE INDEX architecture_index on code (architecture);
CREATE INDEX id_index on code (identification);
CREATE INDEX identifier_index on code (identifier);


# what are the column definitions in global?
sqlite&gt; .schema global
CREATE TABLE global ( 
        id integer primary key on conflict replace autoincrement not null, 
        sign_location text not null, 
        signature blob null 
    );
CREATE INDEX location_index on global (sign_location);


What we're interested in are code.identifier and global.sign_location.

sqlite&gt; SELECT * FROM code WHERE identifier LIKE "%eclipse%";
sqlite&gt; SELECT * FROM global WHERE sign_location LIKE "%eclipse%";


Take a look and make a backup before deleting all matching entries from both queries.

sqlite&gt; DELETE FROM code WHERE identifier LIKE "%eclipse%";
sqlite&gt; DELETE FROM global WHERE sign_location LIKE "%eclipse%";


I've also restarted my laptop, although I don't know if it's really necessary.

That's all!