It seems that the table manipulator node removes these without asking and I can’t do anything about it. It doesn’t matter if the propertie is a reference to a column that is changed by this node or not.
table properties are indeed sort of a poor cousin of KNIME as they are very (very) rarely used - thanks for reporting (internal reference: AP-18138).
Meanwhile, I’d recommend to split up the operations you want to achieve with the Table Manipulator into single nodes, i.e. “Column Resorter”, “Column Rename”, “Column Auto Type Cast”, “RowID”, “Concatenate”, …