Gm Remy developed Modern Arnis and had influences from his family (grandfather), Balintawak Escrima, and some other FMA systems. along with influences in Japanese karate, and here in the states small circle jujitsu (Wally Jay), and catch as catch can wrestling (possibly Rocky's dad) . Although the karate influence maybe more along the line of how to organize and teach larger groups of people, and some inflluence on stances etc. etc.
GM Ernesto had influences from GM Remy, his father, his family, and others as well. Kombatan has 5 main areas of study double stick, single stick, espada y daga (stick and knife), knife, and empty hand. In Kombatan there is a wider study of double stick, espada y daga, and knife work than in Modern Arnis. In Kombatan the material is probably closer to what GM Remy taught in the Philippines prior to his exile to the states.
Here in the states GM Remy taught Modern Arnis and it was adapted to the needs of the people here. So the double stick material was shortened, espada y daga for the most part in the 90's was not really taught much anymore, and the knife work was more jujtisu based.
I base these view points on talks with GM Remy and GM Ernesto. Here in the states, there was no need for double stick, or stick and knife, and the knife material was more for empty hand against the knife. In the states where he hooked up with GM Wally Jay and George Dillman (pressure point karate fame) Gm Remy's Modern Arnis changed some over the years to reflect some of these influences.
So both systems have similar stances, strikes, striking patterns, blocks etc. etc. but they are different as well. Kombatan always had more of a karate (hardcore smash and takedown) feel to it whereas Modern Arnis had more of a jujitsu (higher level locking, take downs, etc. etc.) and a more indepth study of the empty hand/stick connection with locking and takedowns than Kombatan.
I've trained through seminars and such with both GMs and earned rank in both systems so I mean no disrespect to either system, nor am I implying one is superior to the other. I'm just trying to give you a perspective on the systems. There have been some previous discussions on the differences between the systems on this board I believe, so you might want to do a search and read some other threads.