What type of Flash file? the .fla? the .swf? a video .flv?
Individual machines will vary in their ability to handle larger fla files. And I suppose it depends on whether the file is 46MB when the project is 1/4 done or 9/10 done.
Still, it's always a good idea to optimize content going into your Flash .fla.... don't use large, oversized bitmaps that you then scale down once in Flash, use external content... images, videos, etc.
There is always the (GOOD) option to keep the .wav files external and load them in via actionscript.
For example... here is a 1.13MB .fla that produces a 460kb .swf that plays 275MB of mp3s.
...just an example of the HUGE difference of embedding in timeline verses loading via actionscript.
This example uses an xml playlist to "feed" the data into the audio player.
Your final solution will depend on your coding skills... but I'd suggest that you strive to load the audio .wav files from external files. Exact code with depend on whether you are using AS2 or AS3 and whether or not you use xml to feed that data.
Here is a good source for tutorials:
The size of an .fla file is only too large if your machine has problems dealing with it.... 46MB is not necessarily a big file. But as the size of the .fla increases, you run the risk of eventually not being able to Save or Publish the file.
So if the final size is 46MB and you can Save and Publish... no problem.
On the other hand, if you are still working on the file and the size will continue to grow... you may have problems in the future.
Since the main "weight" of the file is sound .wav, you could always keep them as external files and load them only if and when needed via actionscript.