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a.0.s = "titi" means in JSON { "a" : { "0" : { "s" : "titi" } } }. getConfigList has a feature where if it goes to get the list and it's really an object, it will treat the object as a list if the object has numeric field names. At parse-and-merge time in your example, the array has been wholesale replaced by an object because later values for a field override earlier ones. There isn't an "array assignment" feature in HOCON right now. The feature where getConfigList will reinterpret an object was only added so people could create "arrays" via java properties.
Your particular syntax can't be made to work differently without breaking back compat, though perhaps we could invent some (currently-invalid) syntax that would do that. #30 probably covers the idea of adding such a syntax.
version=1.2.1
Given
Expected:
Actual:
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