Issue:
When using action - Item: Glue items, ignoring time selection, Reaper does not initialise the plugins. Plugins with Latency will either cause injected silence or discard samples.
This is particularly troublesome for our users working on game audio using Reaper.
Repro steps:
+Add a short sample with a quick onset as an sample item.
+action - Item: Show FX chain for item take
+Add a plugin that has a variable latency (pm me if you need something, I am using UrsaDSP Boost VST3 beta 1.5.9)
- This will call initialize() and setupProcessing() and then setActive() twice all of which filter through to juce::AudioProcessor:

repareToPlay() which is good as this can set the latency.
+Change the plugin latency - in Boost just make the attack / lookahead longer e.g. 40ms
+action - Item: Glue items, ignoring time selection
- this does NOT re-init the plugin. The plugin then adjusts the latency during IAudioProcessor

rocess and Reaper ends up injecting samples.
I have a feeling that the above might be intermittent*. If it works as expected (without the bug) then follow these additional steps.
+action - Edit:undo (revert the glue and bring back the take FX chain)
+Change the plugin latency from long to short - in Boost just make the attack the other extreme e.g. toggle 40ms <-> 2ms
+action - Item: Glue items, ignoring time selection
+Repeat from undo if required.
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Possible solutions:
Please either re-init the plugin before action - Item: Glue items.
OR
It might offer better plugin compatibilty to process a blank block (after the parameters are updated) to allow plugins that only set latency in the process method to stabilize ahead of glueing the item.
*I suspect you are already doing this, however that blank block is not sent in some cases (after the action - Edit:undo)
Thanks for a great DAW and thanks especially for not being one of the DAWs that tries to forbid debugging!
Dave