I think you are mistaken. The word en is always pronounced [ɛn], the word één is pronounced [e:n] and the word een is has four possible pronunciations: [nən nə ən ə].
When do Flemings say which pronunciation?
1. In Standard Dutch: always [ən]
2. In the dialects:
-Masculine words: nə or nən
nə man, nən auto, nə wagen, nən gameboy, nən dag, nə fiets
(You say nən before words that start with a vowel or T, H, B, D or English g. Otherwise you say nə. However, it depends on the dialect, because in the east you will hear more nə than nən)
-Feminine words: always ən
ən vrouw, ən koe, ən kip, ən kat
-Neuter words: ən or ə
ə koekske, ə pakske, ən boek, ə gebouw, ə meisje
(You say ən before words that start with a vowel or T, H, B, D or English g. Otherwise you say ə. However, it depends on the dialect, because in the east you will hear more ə than ən for neuter words)
3. In tussentaal: As you likely know, many Flemings don't speak Standard Dutch, but they don't speak the original local dialect either. They speak something in between, which is known as tussentaal and depends on the individual. I would say that many Flemings (including me) use the following system:
De-words: ən
Het-words (neuter): ən or ə (as mentioned above)
This is because the words nə and nən are considered dialectal, so they are replaced by ən, but the word ə is kept because it sounds almost like ən. Many people are unaware that they speak like this.