So, thanks for the response first off. It definitely is the case that InDesign creates an encryption.xml file within the META-INF folder, even though there shouldn't be any encryption. We are merely taking a raw .indd, exporting, and cleaning up in Sigil...so, very possibly it could then be some of our InDesign files, as older exports we have done still work fine in the new Sigil.
This is the encryption.xml file:
<encryption xmlns="urn
asis:names:tc
pendocument:xmlns:conta iner" xmlns:enc="http://www.w3.org/2001/04/xmlenc#" xmlns:deenc="http://ns.adobe.com/digitaleditions/enc"><enc:EncryptedData><enc:EncryptionMethod Algorithm="http://ns.adobe.com/pdf/enc#RC"/><enc:CipherData><enc:CipherReference URI="OEBPS/Fonts/AGaramondPro-Regular.otf"/></enc:CipherData></enc:EncryptedData><enc:EncryptedData><enc:Encrypti onMethod Algorithm="http://ns.adobe.com/pdf/enc#RC"/><enc:CipherData><enc:CipherReference URI="OEBPS/Fonts/AGaramondPro-Italic.otf"/></enc:CipherData></enc:EncryptedData></encryption>