The problem can be distilled to a much simpler form to help illustrate what is going on. (whenever you find a problem, try to find the most simple form that shows the problem)
It has to do with definite vs. indefinite integration.
Clear[q, x, L1]
Integrate[q[x]*f[t], x]
Out[52]= f[t]*Integrate[q[x], x]
You see that now it pulled the function that does not depend on the integration variable out.
Do the same, now using definite integration
Clear[q, x, L1]
Integrate[q[x]*f[t], {x, 0, L1}]
Out[54]= Integrate[f[t]*q[x], {x, 0, L1}]
You see, the f[t] remained inside. I am not a math guy, so can't explain why it does not remove f[t] out when it is a definite integration. But it looks like when it is definite integration, you need to tell it that those functions that explicitly depend on t and not x remain independent of x for the definite case. I do not know how to do this.
That is why this gives zero
Integrate[q[x]*f[t], x]-f[t]Integrate[q[x], x]
Out[55]= 0
while the definite version does not (which is what you are basically asking)
Integrate[q[x]*f[t], {x, 0, L1}] - f[t]*Integrate[q[x], {x, 0, L1}]
Out[56]= (-f[t])*Integrate[q[x], {x, 0, L1}] + Integrate[f[t]*q[x], {x, 0, L1}]
Just wanted to point the problem more clearly that is all.
Edit
Additional observation. It seems the simplification does not happen becuase Mathematica does not know that f[x] does not depend implicitly on t. See:
Clear[x,t,f,g,L1]
Integrate[x*g[t],{x,0,L1}]-g[t]*Integrate[x,{x,0,L1}]
Out[14]= 0
Becuase it now sees that f[x] really does NOT really depend on t, then it pulled out g[t] and we get zero.
But when we write
Clear[x, t, f, g, L1]
Integrate[f[x]*g[t], {x, 0, L1}] - g[t]*Integrate[f[x], {x, 0, L1}]
Out[17]= (-g[t])*Integrate[f[x], {x, 0, L1}] + Integrate[f[x]*g[t], {x, 0, L1}]
So, may be some assumptions is needed. Not sure now. Just thought to mention this.
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