It appears to me that one way of storing data in a B-tree as a file can be done efficiently with C using binary file with a sequence (array) of structs, with each struct represe
I did a very quick search and dug up this: http://people.csail.mit.edu/jaffer/WB C source: http://cvs.savannah.gnu.org/viewvc/wb/wb/c/ - it seems to offer disk-based B-tree style databases - although taking a look at "delete.c" it seemed to imply if you delete a node everything down from it would be taken out - if that's the correct behaviour then it sounds like something that might help?
Also - B-trees are often used in filesystems - could you not take a look at some filesystem code?
My own inclination is that of a file-system - if you have a B-tree of fixed-size, whenever you "delete" a node rather than attempting to remove the reference, just set the value to whatever means nothing in your code. Then, have a clean-up thread running that checks if anyone has the file open for reading and if all's quiet blocks the file and tidies up.