This is actually a common theme in the history of writing. Allow me to broadly outline a process (which is not necessarily correct in all cases):
- an ideographic script becomes a logographic script
- there are both phonemic components and semantic components
- a single grapheme can have a phonemic and a semantic reading ("polyvalency")
- a graphemic construct (a written "word") is originally one way in a phonemic reading, but is reinterpreted differently (either later on in the continuation of the same language, or in a different context with a different language).
In this case, we have inversion, then phonemic > semantic reading for the middle glyph [f > snake > wa], then semantic > phonemic in the last glyph [pillar > sh].
I'm most familiar with the East Asian sprachbund / Chinese character-centred world, where this kind of thing would simply be called the "original reading" vs "derived reading". However, more specific terms would be required.
In the Japanese system, step 4 of the above has a clear distinction, interpreted as a phonemic reading (音読み on'yomi) [closer to the original Chinese] or reinterpreted as a semantic reading (訓読み kun'yomi) [based on the native Japanese meaning].
You also have a looser set of readings for Japanese compounds (当て字 ateji) where it is in essence a phonemic reading, but does not exist in the original Chinese. There are also a subset of semantic reading-based compounds (熟字訓 jukujikun) where the several kanji have to be read as one unit, completely separately to the on'yomi and kun'yomi of the individual kanji.
In the Chinese topolect world, there is a similar issue with different terminology. E.g. the lexeme for meat 肉 is hypothesised to have been pronounced *k-nuk or *njug back in Old Chinese. In the Min Nan topolects (stretching from southern Fujian to Chaozhou in Guangdong and across to Taiwan), the derivatives jio̍k / lio̍k / he̍k / hia̍k correspond to *njug from Old Chinese, but they are not the usual word for meat, which is instead bah / mah, with an unclear and possibly non-Old Chinese etymology.
The first "regular" derivative is considered the "literary reading" (文读) whilst the more common but possibly unconnected is considered the "colloquial reading" (白读). The distinction is important for reading compounds the right way, and is better suited to cases where the tradition of reading is more or less uninterrupted, based on the same script, but also within the same language system. Less likely to fit your case here.
Closer to your (Semitic language) world, Sumerian to Akkadian had a very similar relationship with Old/Middle Chinese to Old/Middle Japanese. E.g. the cuneiform for "cow" in Sumerian, pronounced ab, was used in Akkadian for "cow", pronounced littu, and for the sound ab, but then also for the sound lit. This is called "graphemic polyvalency", and occurs in Old Japanese (the man'yōgana 万葉仮名 system) too.
Mayan hieroglyphs adopted into Nahuatl (of the Aztecs) and Zapotec also show similar polyvalency. However I'm not familiar with those spoken languages at all, so I won't comment beyond the existence of the phenomenon there.