LINKAGE and FASTLINK have a constant called maxloop. In order for the programs to run correctly, maxloop must be at least as large as the number of loops in any of the input pedigrees. There are no significant negative consequences for making maxloop larger than it needs to be. In LINKAGE 5.1 and all versions of FASTLINK, maxloop is set to 2 in the distribution; the user is free to increase the value. Rumor has it that some versions of LINKAGE have been distributed with maxloop set to 1.
So far as I can tell, there is no correctness harm in trying input pedigrees with arbitraily large number of loops, so long as maxloop is set at least as large as the number of loops. Depending on the data set, the running time may increase exponentially with the number of loops, but the space requirements will not increase substantially.