Searched the logs. It seems that the resource-.mhtml has refused to be decrypted for quite some time. Saving and reattaching it solved the jex-problem. Removed both the .mhtml and corresponding .md from the cloud and .config by hand. Succesfully. But was unable to do the same to the .md-file. A Nextcloud-thing, perhaps? In Synchronisation Status Joplin Desktop still maintains, that it cannot decrypt the .mhtml - and while syncing tries to decrypt it continously.

Here's the decrypting log of the .mhtml:

2019-08-12 12:08:19: "DecryptionWorker: error for: b540e13769b149ffaa2aa86f03c55058 (resources)", "Error: Error: ENOENT: no such file or directory, open 'C:\Users\.config\joplin-desktop\resources\b540e13769b149ffaa2aa86f03c55058.crypted'. Path: C:\Users/.config/joplin-desktop/resources/b540e13769b149ffaa2aa86f03c55058.crypted
Code: ENOENT
Error: Error: ENOENT: no such file or directory, open 'C:\Users\.config\joplin-desktop\resources\b540e13769b149ffaa2aa86f03c55058.crypted'. Path: C:\Users/.config/joplin-desktop/resources/b540e13769b149ffaa2aa86f03c55058.crypted
at FsDriverNode.fsErrorToJsError_ (C:\Users\AppData\Local\Programs\Joplin\resources\app.asar\lib\fs-driver-node.js:10:16)
at FsDriverNode.open (C:\Users\AppData\Local\Programs\Joplin\resources\app.asar\lib\fs-driver-node.js:137:15)", "{"id":"b540e13769b149ffaa2aa86f03c55058","title":"Kolmekymppinen! Aloita säästäminen vanhuuden varalle nyt – “Ettei eläkkeellä tarvitsisi tinkiä kodista tai terveydestä” _ Yle Uutiset _ yle.fi.mhtml","mime":"application/octet-stream","filename":"","created_time":1557588921947,"updated_time":1557588921947,"user_created_time":1557588921947,"user_updated_time":1557588921947,"file_extension":"mhtml","encryption_cipher_text":"","encryption_applied":0,"encryption_blob_encrypted":1,"size":-1,"type_":4}"

Managed to remove from the cloud. No more upload errors. I also have one note+resource pair (.nomedia) which refuses to be uploaded. Getting sync error even after I both removed the resource from .config/resources and the Joplin-search finds no note instance. Neither can be found in the cloud.