It would not be easy to convert such a document in a non-plain-text format with proper linked notes and note references.
How the note references are marked in your plain text document? Something like this?
main body text – main body text – main body text
 note text - note text - note text
In any case, if these documents are important to you, you can email them to support@AtlantisWordProcessor.com
. We could try to convert your documents to the required format, and send the converted document files to you.