I am using the dataset provided for LOLA to analyze my data (hg38). In the files generated when saving the results with writeCombinedEnrichment I see new columns:

dataSource              filename
ENCODE segmentation Helas3_T.bed

What are these .bed files and where to find them?

In the website there is a link to https://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/ but that file or similar files are not present there. Even after accounting that narrowPeak is a .bed format, there are just three files about Helas3 wit no mention of T: wgEncodeAwgTfbsBroadHelas3CtcfUniPk.narrowPeak.gz, wgEncodeAwgTfbsBroadHelas3Ezh239875UniPk.narrowPeak.gz wgEncodeAwgTfbsBroadHelas3Pol2bUniPk.narrowPeak.gz

The default LOLA database has files from multiple sources. The ones you're referring to are from segmentations, It was many years ago that I assembled that database, but I believe those ones came from the Segmentation tracks from UCSC -- I think this was probably the ChromhmmHelas3, or maybe the CombinedHelas3 segmentation, and T would have been the state called for those regions by that segmentation.

You can find the original files here: https://genome.ucsc.edu/cgi-bin/hgFileUi?db=hg19&g=wgEncodeAwgSegmentation

Let me know if this doesn't answer your question, and I can dig a bit deeper.