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For the future - PLEASE
- provide representative samples - AND STICK TO THEM!
- provide a detailed and specific description of your problem - DON'T reference ID not explaining what that is, explain...

Try
sed 's/[~>]/&#/g' file | sort -t"#" -k5,5 | sed 's/#//g'
179341~1704509~1704480~456690129_TOTAL->BTT TOO
179341~1704481~1704480~475919266_TOTAL->MANUAL->COM...

"the last record" - even if I translate "record" to "field", "MANUAL" would NOT be the last.

"group record based on the entire row" - what does this mean? Is that bespoke subfield the key, or the...

Applying copious amounts of phantasy, (or wildly guessing, whatever you prefer) let me try to paraphrase your request, which, btw, dramatically changed during the course of the thread:

A file of...

With a ">" separator, there's no 4th field to serve as a sort key in above data. I'm sorry, I don't get what you're after.

Please be aware that a sort key by default stops at line end; to confine it to a single field, the stop position needs to be specified as well, e.g. -k4,4. Also note that it's a lower case k .

What do you mean by I can sort by each column and pipe it to next K2 ?

Try
sort -t">" -k2 file
456690129_TOTAL->BTT TOO
-172680236_TOTAL->BTT TOO->MTO
-1903630442_TOTAL->COLE
475919266_TOTAL->MANUAL->COM
-541283452_TOTAL->MANUAL->CRT
-572275295_TOTAL->MANUAL->MTO...