I think you're going to have to give up a little more about what you're actually doing.
I agree with Jason. Why are you running these batch processes? What do they do? Maybe a FileMaker Script can provide substitute functionality if we know what it is you are trying to accomplish.
Okay, for instance in one place I have a list of sales items. A sales rep can look through the list and click on the selection button and when completed he goes up to a selector on the header and selects "Make Sales Entries for All Selected Items". This fires off a script which then makes an entry in the sales table for each item which was selected and then deselects all of the items. There are multiple batch commands he can do once he selects each of the items.
The same thing can be accomplished with a FileMaker Replace Field Contents script step. The only concern is record locking. If someone else is editing one of the records then that record will not be modified.
So currently every record has a field for the purposes of marking the record as "selected". And yes this is going to cause both record locking issues and problems when different people are trying to select different records in similar lists.
Get rid of that field. Use a button to select/deselect the record. When you select the record, you just want to add the record key to a return-separated list in a global field. Use conditional formatting to show you if the record is selected or not.
This means the items table is never modified, and there is no conflict between multiple users.
You'll need to remember to deal with (or prevent) situations where old selections are in the field even though they're no longer in the found set (so you won't "see" them as selected).
For deselecting records, you'll have to substitute out the id, which means you should either put start and stop characters on each line, or make sure there's a carriage return at the beginning and end of the field.
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For working examples of what Jason is describing, take a look at the "check boxes with scroll bars example in the following file. You don't have to use a portal for this technique as is done here, but if you look at the script that fires each time an item is selected or deselected, you'll find a calculation that either adds or removes a selected item from the return separated list used to track which items are selected.