What is the difference between fixation and loss of alleles in a population?
Yes, 'lost' seems to be referring to fixation of the a allele in this program, where the statements 'fixed' and 'lost' are specifically referring to the A allele. Conceptually, 'fixed' and 'lost' are describing the same thing in this particular case ( since you only have two alleles in the population) - the loss of one allele in a population.


  Note that once the plot of the gene frequency curves reaches the right-hand side of the graph, the program prints there the number of populations that fixed for the A allele (ended up with a frequency of 1.0) and the number that lost this allele.


(my emphasis, from http://evolution.gs.washington.edu/popgen/popg.html)