Apologies if this has been asked before. I am a beginner at NGS analysis and could not find anything similar.

I am dealing with 4 fastq files: 2 runs each with a single and paired end file. They contain 3 multiplexed PCR amplicons. I used the barcode splitter from the FASTX toolkit to demultiplex them and it worked well. I next want to use cutadapt to trim primers. However, when using cutadapt on the files generated after the demultiplexing, I get an error that this cannot be performed as the files might be truncated. My questions are as follows:

1. Is something wrong with the format of the files after using the barcode splitter? Can I fix this?
2. Ideally, I want to work with a single merged file and sort relevant data (half of the single and paired end reads are likely to be useful for my purpose). I am not sure if I can simply merge 2 different runs with single and paired reads into one file. The other option would be to run the barcode splitter individually on the 4 files. Then combine the resulting files belonging to one barcode together from both runs and reads. How do I go about this?

Thanks for the time and all advice will be much appreciated.