Error messages and disappearing audio wavs

Hello, I have been working on a book that is rather large (although I have worked on much larger). Originally the DTB consisted of just chapter 1. I opened chapter 1, and "saved as" under the new folder chapters 1-3. I then continued building the book, importing the pre-recorded audio files of said chapters. I have done this exact process in the past without issue. When I got to the very end, each time I split the last 2 sections (of maybe 50 sections in total) into phrases, other sections waveforms would disappear. I could still play the section, but there was no waveforms next to it. If I save it and re-open it, it is the last 2 sections that have no waveforms, and yet I can still play them. I decided to try and export regardeless, as it still seemed to play alright. I exported as Daisy 2.02, and it worked in Amis. HOWEVER, when I went to convert to MP3, I got the following error message. org.daisy.pipeline.core.script.datatype.DatatypeException: Input file 'C:\Documents and Settings\atweedy\My Documents\Obi Daisy\Introduction To Language Chapters 1-3' does not exist. at org.daisy.pipeline.core.script.datatype.FileDatatype.validate(FileDatatype.java:44) at org.daisy.pipeline.core.script.JobParameter.setValue(JobParameter.java:74) at org.daisy.pipeline.core.script.Job.setParameterValue(Job.java:142) at org.daisy.pipeline.lite.PipelineLiteCLI.createJob(PipelineLiteCLI.java:193) at org.daisy.pipeline.lite.PipelineLiteCLI.main(PipelineLiteCLI.java:102)