Well, to be frank I am trying to help while seeing “through a glass darkly”, so I’m not sure exactly what is what. I have the impression that when you work in Profile 2, changes made in the browser extension are indeed reflected in the Web Vault (and vice versa) — thus, I am considering this to be the “main” vault (or perhaps “canonical” is a better descriptor).
It is synchronizing data with some cloud database — sending saved changes to that cloud database, and receiving a current copy of the database data when you log in after having logged out.
My suggestion would be to create CSV exports from both profiles. Open each in a spreadsheet app (e.g., Excel), and insert a new column before the first column, giving the new column the title “Source”, and entering the value “Profile1” in every non-empty row of the Profile 1 CSV, or the value “Profile2” in every non-empty row of the Profile 2 CSV.
Next, create a new spreadsheet, copy the contents of both CSVs into the new spreadsheet (pasting the second set of data just below the first set of data, ensuring that the columns are aligned), and delete (or simply do not transfer) the row of column titles from the second CSV. Also create a second such combined spreadsheet, with the order of the source data reversed (i.e., which profile data is on top vs. on the bottom).
Finally, you can use the spreadsheet app’s de-duplication feature on both of the combined data sets, and then look at rows on the bottom, for which the value of the “Source” column equals whatever profile was the second one added to the combined spreadsheet. This will tell you the items that only exist in that profile, allowing you to identify missing items.
If you need help using the available de-duplication tools, please let me know what app you use for spreadsheets.