That will depend upon the pointers and how they are programmed into that game, or indeed file if a game has multiple formats.
Some of the older tools like atlas and maybe some of the Russian efforts (see kruptar 7 and oriton,
https://romhack.github.io/doc/kruptarPlugins/ is for plugins but can serve as a bit of an overview) can struggle as they are aimed more at things working within a memory bus than at file level like most DS stuff.
Do make sure you can't abuse a spreadsheet first of all -- many times a game will end a section with 00 or something obvious that does not appear (or only appears a couple of times and thus can be manually deleted) in the rest of the text section. With that in play you can instead then do a search with whatever hex editor supports such things (I like hex workshop here but there are others, can probably also do a binary grep if you really wanted) to get a text list of locations of 00 or whatever indicator you have.
If you know the pointer format* then should not be too hard to figure out a new pointer list from the search noted above and go from there.
*standard, offset and relative being the big three.
Standard are just numbers that count from the start of the file. Offset tends to be it starts from a given section (usually the text section) so it just a simple subtraction from the list generated above, and relative where the pointer value is added to the current location/location of the pointer itself in the file (there are reasons for doing this in coding as it can be faster). Relative are not so common and easy enough to spot -- if you line up the original file locations of end of text sections then each new line will be out by a further fixed amount (if you are starting from the start and each value is say 4 bytes then you will be out by 4,8,12,16,20.... bytes).
There are other things like I have seen shifted pointers (touch detection and various aspects of 3d files here), and some pointers will use bits in them to indicate things (NARC archives quite notably use the upper bit to indicate a subdirectory as DS game files will tend not to need the full 32 bit address range) or have bits in between pointers to indicate formatting or maybe just length values. This also says nothing of things like Wizard of Oz where the whole thing was a quasi scripting engine and each segment (think linked list) had a length value.
After that then yeah manual work, you build a tool to fix it as you are editing things.
