In most cases, it's preferred for a letter to represent a phoneme, the smallest meaningful unit of sound. For instance, English "cat" /kæt/ has three phonemes, /k/, /æ/, and /t/. Changing any one of those to another phoneme could change the meaning.
Silent letters can be justified in a language's native script, if the letters used to represent a phoneme that was lost because of sound changes. For example (if the Latin alphabet is your language's native script and not a transcription), <h> might have represented /h/, and <'> /ʔ/, but perhaps both phonemes were lost through lenition.
N'hésite pas à corriger mes erreurs.