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I found a bug in phone.es.inc file:
Validation function (valid_es_phone_number) works OK (I didn't try every possible combination, but for me there was no bugs until now...), but format function (format_es_phone_number) converts any inserted phone number into an string with two characters (two blank spaces) before inserting into database because of the preg_match function in line 68.
In order to fix it temporarily , just comment the line 71 and it won't delete the number, but no format is applied (inserted value == shown value):
// $phonenumber = $matches . ' ' . $matches . ' ' . $matches;
I also attached a patch for this temporary solution