That's a simple split by clause with a bit of handling for the wildcard case cookie1
index=someindex container_name=app ( cookie=*cookie1" OR cookie="cookie2" ) event=Someevent
| rex field=cookie "(?<cookieType>cookie\d)"
| timechart span=1m perc50(latency) by cookieType
The rex statement is looking for the 'cookieX' where X is a digit and creating a new field called cookieType containing either cookie1 or cookie2 and then the by clause will split the result into the two lines on the chart.
If you actually want two charts in the same panel, then select the 'trellis' mode and choose the aggregation, which will give you two separate charts in a panel, with the cookieType on each chart. If you just want two lines in the same chart, ignore the trellis mode