Can't Swap locomotives in Scenarios

Hello, I'm trying to swap out some locomotives in scenarios, but the changes seem to revert whenever I click something other than the item I changed. For example, if I'm trying to replace an engine, I click the consist, then click the engine to be replaced, then click the engine I want to replace it with, and hit swap selected items. The item will change,m but then if I click on another consist, the item I swapped out will be back. This is on older, non .ap file routes.
I've copied the three files from the railworks folder to the rw_tools folder as indicated in the help file, I've set all files in the railworks folder to not be read-only, and I re-downloaded the latest version tonight. I'm still on the trial.
Also (maybe related?), when I click on consists, I often get notified of missing .bin files, even for pieces of rolling stock that I know I have and are working ok.
I feel like I'm likely missing something really obvious here, although not obvious enough that I've been able to figure it out!
EDIT: When I loaded up one of the scenarios I was trying to edit, the consist changes I tried to make had been made, but RW_Tools still shows the old consist...
Thanks
I've copied the three files from the railworks folder to the rw_tools folder as indicated in the help file, I've set all files in the railworks folder to not be read-only, and I re-downloaded the latest version tonight. I'm still on the trial.
Also (maybe related?), when I click on consists, I often get notified of missing .bin files, even for pieces of rolling stock that I know I have and are working ok.
I feel like I'm likely missing something really obvious here, although not obvious enough that I've been able to figure it out!

EDIT: When I loaded up one of the scenarios I was trying to edit, the consist changes I tried to make had been made, but RW_Tools still shows the old consist...
Thanks