Since a few hours, I'm dealing with a really weird case:
A few weeks ago I developped a Power BI solution and originaly I just needed to refresh the data and upload it to PowerBI.com After the refresh Power BIDesktop has no problem with my data, it's justhappy, displaying the correct charts and the data are correct. When I push on Publish, I'm asked to replace or not the existing file and then after a few seconds, I'm receiving a message such as "failed to upload, unknown error" with a requestId and the nice button "send a frown".
I've tried to remove the tables one by one and uploading my file until I identified the tables with a problem. When removed I've no problem to upload. I continued to investigate these 4 tables and clearly identified that my problem was in merge (left outer). My first idea was that it was a data issue so I applied a "Keep first rows" set to 0 ... on both tables but it didn't fix the problem. I tried a few other things (change to inner join, change the original data type in my SQL query from a nvarchar(510) to varchar(20)) and the problem was still there. Finally I decided to change the table to merge and to try with another table (and another field) ... no problem. I've other merges in my solution and they are working fine.
Have you tried to pull the file in from Power BI online and do you experience the same issue? Just curious; it sounds like it is specifically about the Merge statement but a work around might be to Get Data -> Files -> PBI file. Our model is based on SSAS tabular in AWS and Azure; i have experienced a similar issue after a release and this was something that worked for me.
It seems like this is a strange and rare issue that you should open a ticket for. I'm sorry I couldn't be of more help; the only other thought was to put it in one drive and see if that works. Based on your testing it looks like the left outer join is the cause.