Pilon version 1.24 has one algorithm change which affects local reassembly solutions, particularly when using diploid data. Previously, if there were several equivalent solutions for a local reassembly (gap fill or continuity break fix), it would pick the first available solution. In v1.24, it picks the smallest change among equivalent alternatives, preventing it from including surrounding heterozygous (or ambiguous in the haploid case) SNPs in a larger changed block. This reduces both the size and number of BreakFix solutions in the output from diploid data, since many of them contained spurious differences related to heterozygosity.
Support for the experimental --threads option has been removed. It was implemented by an ugly hack which no longer works in modern scala, and it was a resource hog in any case. I hope to revisit multithreading again in the future.
Otherwise, v1.24 is a maintenance release, updating the code to compile on scala 2.13 and updating the htsjdk library version to 2.23.0, allowing support for newer file formats such as csi indexes. Additionally, v1.24 was build using the Java 11 toolchain, so I recommend using a JRE version 11 or greater.