I just started using Ubooquity and it's still working its way through my collection.  Looking at the logs it appears that most (if not all) PDFs fail to be added.  Here's an example from the logs:

20191222 09:42:59 [Scanner thread] ERROR com.ubooquity.data.feeder.a - Failed to insert Z:\Vault\Books\Comics & Manga\Legend of Zelda\The Legend of Zelda - Majora's Mask & A Link to the Past [Eng TPB].pdf
java.lang.OutOfMemoryError: Java heap space
   at java.util.Arrays.copyOf(Unknown Source) ~[na:1.8.0_231]
   at java.io.ByteArrayOutputStream.grow(Unknown Source) ~[na:1.8.0_231]
   at java.io.ByteArrayOutputStream.ensureCapacity(Unknown Source) ~[na:1.8.0_231]
   at java.io.ByteArrayOutputStream.write(Unknown Source) ~[na:1.8.0_231]
   at org.apache.pdfbox.io.IOUtils.copy(IOUtils.java:68) ~[pdfbox-2.0.6.jar.6729965043262619269.tmp:2.0.6]
   at org.apache.pdfbox.io.IOUtils.toByteArray(IOUtils.java:50) ~[pdfbox-2.0.6.jar.6729965043262619269.tmp:2.0.6]
   at org.apache.pdfbox.pdmodel.encryption.SecurityHandler.decryptStream(SecurityHandler.java:449) ~[pdfbox-2.0.6.jar.6729965043262619269.tmp:2.0.6]
   at org.apache.pdfbox.pdfparser.COSParser.parseFileObject(COSParser.java:785) ~[pdfbox-2.0.6.jar.6729965043262619269.tmp:2.0.6]
   at org.apache.pdfbox.pdfparser.COSParser.parseObjectDynamically(COSParser.java:742) ~[pdfbox-2.0.6.jar.6729965043262619269.tmp:2.0.6]
   at org.apache.pdfbox.pdfparser.COSParser.parseObjectDynamically(COSParser.java:673) ~[pdfbox-2.0.6.jar.6729965043262619269.tmp:2.0.6]
   at org.apache.pdfbox.pdfparser.COSParser.parseDictObjects(COSParser.java:633) ~[pdfbox-2.0.6.jar.6729965043262619269.tmp:2.0.6]
   at org.apache.pdfbox.pdfparser.PDFParser.initialParse(PDFParser.java:241) ~[pdfbox-2.0.6.jar.6729965043262619269.tmp:2.0.6]
   at org.apache.pdfbox.pdfparser.PDFParser.parse(PDFParser.java:276) ~[pdfbox-2.0.6.jar.6729965043262619269.tmp:2.0.6]
   at org.apache.pdfbox.pdmodel.PDDocument.load(PDDocument.java:1000) ~[pdfbox-2.0.6.jar.6729965043262619269.tmp:2.0.6]
   at org.apache.pdfbox.pdmodel.PDDocument.load(PDDocument.java:956) ~[pdfbox-2.0.6.jar.6729965043262619269.tmp:2.0.6]
   at org.apache.pdfbox.pdmodel.PDDocument.load(PDDocument.java:904) ~[pdfbox-2.0.6.jar.6729965043262619269.tmp:2.0.6]
   at com.ubooquity.fileformat.pdf.b.a(SourceFile:34) ~[Ubooquity.jar:2.1.2]
   at com.ubooquity.b.d.a(SourceFile:62) ~[Ubooquity.jar:2.1.2]
   at com.ubooquity.data.feeder.a.b(SourceFile:531) ~[Ubooquity.jar:2.1.2]
   at com.ubooquity.data.feeder.a.b(SourceFile:468) ~[Ubooquity.jar:2.1.2]
   at com.ubooquity.data.feeder.a.b(SourceFile:112) ~[Ubooquity.jar:2.1.2]
   at com.ubooquity.data.feeder.a$$Lambda$5/16085064.run(Unknown Source) ~[na:na]
   at java.lang.Thread.run(Unknown Source) ~[na:1.8.0_231]

Just wanted to share the PDF OOM errors I'm seeing. I doubt it will help, but it can't hurt.