I have the same issue, and while I hate it, I'm glad to see I'm not alone. And it is scary, putting some of my most sensitive data in the protected note and then discovering that it's gone. Not only that but where did it go? Floating around freeform on some Apple Server? - or worse?
Anyway, I haven't seen any fixes or causes from other users so figured I'd info on onto the Community Cloud and hope a solution will appear. In my case, this issue just showed up a few weeks ago. I'd used the protected note for months without any problems. I figured I must have done something stupid like unwittingly deleting the table when I was trying to do something in one of the other protected notes. So, about a week ago I put the table back in the note and it was OK on my iPhone as well as iCloud. Now today, I see it is gone again.
I'm running Mojave 10.14.6 on my Mac Mini, iPhone 8 iOS 13.3. And by the way, I can't upgrade to Catalina yet - I have to find solutions to replace 7 apps that are not available in 64bit versions.
Here was my workflow. All of this was done on my MacMini. The source for the missing tables were password protected Excel files that stored in my Documents folder, which is synced to iCloud. I opened the Excel file, selected the cells in the spreadsheet, right click copied the cells to my Clipboard, opened the Apple Note put my cursor into the note and right click pasted the clipboard. The information transferred as a table into the Note. Pretty straightforward and simple I think. As I noted above, I repeated this about a week ago when I discovered the missing data in the file and all seemed OK. Now, the table is apparently gone from the note.
While I realize Notes is a free app - becoming quite feature rich and tremendously useful, it must protect my data if I'm to rely on it. And understanding the cause as well as the failure mode is very important moving forward - is it Notes?, is it iCloud, is it Sync?, is it my iPhone?, is it my Carrier?, is it my Network? Since I'm posting, I'm including a couple of aside grumps. First, all protected notes open when any one is opened - that may seem convenient, but I believe it carries too much risk. And second, apparently there is no version history for Notes so that precludes looking back in time to discover the prior state of any note.
Thanks for wading through my post.
Hoping for a solution or workaround from Apple or the community.