Hum, I don't use Amazon for subtitles.
Maybe a hint to help you, using notepad++:
Open your ass file (or the text you want to convert to Amazon format) in notepad++
Use Ctrl+H, activate the regular expression search mode, and use (without quotes)
find : "(\d:\d\d:\d\d)\.(\d\d)"
replace : "\1,\20"
Click on "replace all"
That will convert every text with a shape "0:00:00.00" in the file to a shape "0:00:00,000" (that will change the dot to comma and add a suffix "0" to the result).
This could be a workaround for you.