If you create an input for a line item in the header logic (through quoteProcessor.addOrUpdateInput()) and create a quote revision, the values from the inputs disappear.

This happens only for line items; when added to ROOT, the inputs preserve their values.

for (lineItemMap in quoteProcessor.getQuoteView().lineItems) {
    if (lineItemMap.folder) continue  //skip folders
    
    quoteProcessor.addOrUpdateInput(lineItemMap.lineId,
            ["name"     : "SampleInput",
             "type"     : InputType.STRINGUSERENTRY,
             "required" : true
            ]
    )
}

The desired behavior somehow conflicts with another standard behavior. 

The solution is to have an input defined at the line items level.

The code snippet here can be fixed just by adding a single formula element to the calculation logic for a line item:

api.stringUserEntry("SampleInput")

Then the header logic can even stay as is. 

With this change, the input exists in the revision too.