Inflated TE counts and masked bp in EDTA annotation after removal of part of the genome

[Nyasita]

Hi, I have used EDTA to annotate TEs for my plant genome. Initially, I had 12 chromosomes and I ran EDTA but then I got rid of one chromosome that we suspect to be something else and re-ran EDTA. Now my point of contention is I'm getting rather inflated counts and number of bp masked for the 'smaller' genome. Basically, I would expect with 11 chromosomes in my genome, the numbers of particular TEs and the bp masked would be less than what was observed for 12 chromosomes.

I ran the code with --sensitive 1 --anno 1 --evaluate 1

Below is a table showing the counts. The counts in brackets are from the run with 12chromosomes and the highlighted values are where i observed inflated values in the smaller genome,

I also removed the 'suspect' chromosome from the gff file i had obtained from the first run with 12 chromosomes genome and computed the results using the protocol here, and got very different results from the actual run (results shown in the table below; again the values in brackets are from the run with 12 chromosomes and the difference is between the unbracketed values in the table below and the table above) . What would be the explanation to this disparity?