I think this is what you should do, but I might be off.
(I have assumed an Auto Increment ID for all tables)
This is the easy part, appending the values from
Master2
into
Master1
insert into Master1 (SrNo) select SrNo from Master2;
Then I think you should actually delete all rows in Trans1 and then insert new ones.
delete from Trans1;
insert into Trans1 (Master1_MasterID) select MasterID from Master1;
The reason is that the values in table Trans2 has no meaning anymore, so no point in merging Trans1 and Trans2.
As I said, maybe I am totally off here and think to simple.