Takiyyudin phonology

So I was musing about vowel harmony, and wondering, what's it look like
when it starts bleeding into consonants, so I threw together this here
baby conlang.

The vowels are organised into two groups, 'green' and 'blue'; the names
don't mean anything, obviously. Some of the consonants take different
forms depending on the colour of a word. In the table below, consonant
PAIRS indicate the blue form followed by the green form. The affricate
TRIPLETS are (almost) simply a shorthand for two overlapping pairs; blue
<chetsun> corresponds to green <chwe'chon>, except in a few cases where
the simple postalveolar form doesn't alternate (thus green <che'chon).

Inventory, with doubled lines for cxs, sometimes:

Blue vowels:  i e  a  u u'
Green vowels: i e' o' o u
u' o' e' are /U O E/; I prefer to write them with the Vietnamese horn
diacritic but that's obviously not good usage on the list.

Consonant system:
p-qu   t   ts-ch-chw   kh
  k^w  t^h    tS tS^w  x

       d   tz--j-jw    gh-g
       t      dZ dZ^w  G  g

           s--sh-sw    h
              S  S^w
m      n               ng /N/

w      r   l           y /j/

Syllables are CV(C), except initial syllables which may be onsetless.
Codas may be <s sh sw h m n ng r l y> or a gemination of a stop. Nasals
don't have to assimilate with following consonants.

So, a question: in languages with harmony, is it common for affixes to
force the rest of a word into a particular form? I'm thinking about
including some that have -only- a green or blue form, possibly because
(fake-historically) they were borrowed from some other language and not
well assimilated.

Hmm.

--
Shreyas

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