Some features that record the edit history of a sequence store the information in a non standard Genbank feature. If you need to export your sequence as a "pure" Genbank you can use FILE | EXPORT | Genbank Flat (strict). This will remove all non standard terms and export a file that is 100% compliant with the Genbank specification.
In the Assembly Editor there are further export options. You can export individual reads, the consensus or more. When you select either FASTQ or FASTQ by default the entire alignment is exported in that format. Reads are padded with gaps to maintain an alignment.However, if you select specific reads (even if this is ALL reads in an alignment) the individual reads will be exported without any padding.
If you need to save from the Results window or export Graphics then use the FILE | EXPORT TAB CONTENTS AS...