How busy that table or database is? If you have users continuously using that table and running queries all the time, it will affect the shrink process and slow it down. If you have a weekly or monthly downtime period and your request is not an urgent one, you may be better shrinking the file that time or maybe during off peaks hours.

Now, regarding to which file the data will go (assuming you have three files and you're emptying one) I think that the data will be evenly dispersed to each of them because both of them are available and they have free space. But I am not so sure about that.