I started my first multi-night project in Siril. It was a little unintuitive on how to do this. First, you’ll want to create sequences for the data from each night, and then preprocess the files. Make sure these sequences have the same name.
However, you want to index the files in each sequence such that one sequence numbering starts where the last one left off. For example, start with creating a sequence at index 1. This can be specified in the text box next to the sequence name in the File Conversion tab. After that sequence is processed and preprocessed, start your next night’s sequence at the next index. That is, if your first sequence had 250 images, start the second sequence at index 251. Convert and preprocess this sequence as normal.
Next, you will need to copy all of the preprocessed files from both nights into a single directory. Change the working directory to wherever this is. In the Sequence tab, check the “Force .seq recomputation” checkbox and click the “Search Sequences” button. This should find all of your files and combine them into a new sequence, which you can continue processing.