Your regex works for me:
$ cat foo
ironia/ironia/S-FS (/(/PU lo/lo/PQMS soprannomineranno/soprannomina
+re/V-P3IF "/"/PU Pique/pique/SP la/lo/RDFS lune/luna/S-FP "/"/PU
+ a/a/E causa/causa/S-FS della/di/E-FS forma/forma/S-FS del/di/E-
+MS suo/suo/A-MS naso/naso/S-MS
$ cat foo | perl -pe "s/-\w{2,}//; "
ironia/ironia/S (/(/PU lo/lo/PQMS soprannomineranno/soprannominare/
+V-P3IF "/"/PU Pique/pique/SP la/lo/RDFS lune/luna/S-FP "/"/PU a
+/a/E causa/causa/S-FS della/di/E-FS forma/forma/S-FS del/di/E-MS
+ suo/suo/A-MS naso/naso/S-MS
If you want to modify the file in-place, take a look at the -i switch
Update: I didn't notice that you want to delete all occurrences. ikegami++
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