Please provide more specific guidance than "smaller batches." Does that mean 60 or 100 or 200 or ...?
Unfortunately, there are no specifics that I can give you. The best that I can suggest is that you use some trial and error to figure out what is safe for your system. If you find that JuiceboxBuilder does not crash when adding 250 images at once (for example), then it would be safer to limit your batches to 200 images at a time (to factor in an element of safety). I realise that this is less than ideal but it should prevent the application from crashing when you near the end of adding your batches.
What is the relevant measure of "smaller"? Number of images? Total size of all images selected? Something else?
I expect the relevant factor is the total filesize of the images in the batch but this is just speculation on my part. I have no access to the JuiceboxBuilder source code and do not know the exact reason for the problem (so cannot easily figure out a 100% safe workaround).
Please enhance the sofware with a warning that too many files are being added and tell me to select fewer. Don't just crash! Check when the crash becomes likely and let me have another chance.
The developer are aware of this issue but I do not know when it might be addressed.
To collect more data on the issue, please let me know how many images you can add before the application crashes and what the total filesize of the batch is.
Also, please let me know what platform (Mac vs PC), operating system/version (e.g. macOS 10.13 or Windows 10 1809) and architecture (32-bit vs 64-bit) you are using and how much RAM your system has.
Thank you.
Does the Lightroom plugin have the same limitation?
No. As far as I am aware, the problem is a limitation specific to Adobe AIR (the platform on which JuiceboxBuilder runs).
If not, is there a way to collect all the settings and apply them in LR?
There is no way to migrate configuration option values from JuiceboxBuidler to Lightroom but, once you have a gallery set up in Lightroom, you can save the settings as a template and apply the template to future galleries (just like a 'Preset' in JuiceboxBuilder).
To set a template in Lightoom:
Once you've got a gallery configured that way you'd like it to be in Lightroom (using the individual controls in the Lightroom plugin's interface), you can save the combination of configuration options as a Lightroom template by clicking the + sign to the right of the text 'Template Browser' (in the left panel of the 'Web' section) and selecting a name for the template.
At any time in the future, if you want to apply this combination of configuration options to a gallery, expand the 'Template Browser' control panel, scroll down to the 'User Templates' section and select the template.