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It has to be a single contiguous array. So, individually selecting 2300 elements, even if done, would still not work.
You will have to remove the missing rows.
It shouldn't be that hard. Add a new temporary column with the formula =ROW() in it. Copy this column and paste back as values only.
Now, sort the data on the X values. All the empty cells will be together. Delete these rows.
Do the same for the Y values.
Finally, sort on the new column. This will return the data to the original sequence. Delete this temporary column.
You can even record a macro doing the above and use it if you have to deal with this issue repeatedly.
Finally, I imagine one could write a wrapper function for LINEST to exclude empty cells or cells with error.