When you load a Scientific Notebook document with Scientific WorkPlace, these elements are lost:
Scientific Notebook has a collection of note types in addition to footnotes and margin notes, but these additional notes are not recognized by Scientific WorkPlace. They are written to the file as #85#>customnote. You can provide a definition of #86#>customnote in tcilatex.tex if you want these to print as either footnotes or margin notes. For example, you could use the definition #87#>def#88#>customnote#1#2{#89#>footnote{#2}}.
Units are written to Scientific Notebook files use the #91#>unit macro. This is not recognized by Scientific WorkPlace. If you want to print documents containing units using TeX, you should provide a definition of #92#>unit. For example, you could define unit with #93#>def#94#>unit#1{#95#>mathrm{#1}}.