Do you know the difference between Tables/Join and Tables/Update ?
If there are multiple matching rows in the source table, Tables/Join fills the cells of the merged column with the value of the FIRST matching row - Tables/Update fills the cells with the value of the LAST matching row. (actually it fills it step by step with the values of all matching rows and the last one sticks: https://community.jmp.com/t5/JMP-Wish-List/Speed-up-Tables-Update/idc-p/654965/highlight/true#M4551).
If you are afraid of outlier values and you cannot be sure that none of them is in a FIRST or LAST position, both variants can be harmful.
To be on the safe side, you should first aggregate the values of the update table so that for each row in the main table, there is only one matching row with a well-defined value to merge.
I like the median aggregation - it's very robust in the presence of outliers. Other options are mean/average or mode (most common entry). But wait -what if there are character columns in the data table that you want to "boil down"? how do you "average" character values?