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In English, "a" becomes "an" when it is followed by a word starting with a vowel sound. A similar thing occurs in Spanish with the word "y", which becomes "e" when preceding a word starting with an "i" sound.

I have searched online and have found educational resources about which situations these specific substitutions are made in. But I haven't been able to find any information about this phenomenon in a broader sense.

Is there a general term in linguistics for words like this, which are replaced by other words in contexts where the next word starts with a particular sound?

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    We use an before a vowel to avoid a hiatus. Are you asking about Epenthesis? – Mellifluous Feb 19 at 4:01
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    @JoyfulSadness Clearly not epenthesis, since Spanish y > e does not involve epenthesis. I expect lexical tone sandhi in Chinese (i.e., where 一 ‘one/a’ becomes before tones 1-3 and before tone 4, and 不 ‘not’ becomes before tone 4) would count as the same category here. The overarching term would be dissimilation, though as a category, that’s much too broad, consisting primarily of cases that aren’t function words of this type. I don’t know if a term for this category specifically. – Janus Bahs Jacquet Feb 19 at 9:29
  • @JoyfulSadness Well, historically, it is rather the deletion of the /n/ before consonants than the emergence of an epenthetic /n/ before vowels. – jk - Reinstate Monica Feb 19 at 11:27
  • @jk-ReinstateMonica: I know that (didn't want to complicate things for the OP). – Mellifluous Feb 19 at 11:29
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    The general term is allomorphy. We say /ə/ and /ən/ are allomorphs of the same morpheme that are in complementary distribution. Similarly, /ðə/ and /ði/ are allomorphs of the same morpheme, both spelled the, but pronounced differently. And then there are irregular suffixes, like the plurals in oxen and sheep, which are allomorphs of the {-Z₁} noun plural suffix. – jlawler Feb 19 at 17:21
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The term you are looking for is probably sandhi rules¹. Sandhi is not necessarily restricted to short words, it can in principle apply to any word.

Examples for languages with rich sandhi rules are Sanskrit and the surviving Celtic languages with their mutations.

EDIT: Another term that is relevant here ist clitic, and there is a process named grammaticalisation that turns full words into affixes via the intermediate step of clitics. This process is specific to short words, long words will be shortened before entering the cline of grammaticalisation.

¹ The link goes to the German wikipedia because their description is in a better state than the English one.

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