Hi @vanjoe
the #REF! error is shown when the following cell does not exist. But it may also happen when rows are reordered like in this case [GH #1975] Sorting issue with HandsonTable when using the compareFunctionFactory function - #6 by adrian.szymanski.
While it is correct (specified by Excel as well) to show #REF! error for rows that are not there, row ordering should be fixed (this is already reported as a bug).
Now within the filters rows are not removed and the reference should be accessible. This can be tested here handsontable (forked) - StackBlitz.
Example
When I type =A1 in the last cell
then I filter the A1 out
I am still able to see the A1 value in the last cel of the B column
So, there might be a different case in your example. Could you please share a demo where the issue can be replicable?