The solubility test showed that the polymer has been crosslinked since it didn't dissolve; however, The FTIR spectrum doesn't show the ester peak (which is the proof of crosslinking of my polymer).
You don't explain your chemistry... but a small number of cross links (~3-5%) can change solubility. So your ester carbonyl may be smaller than you expect.
The chemistry involved or the method needs to be shared in order to suggest something significant. Until then, there can be number of factors which led to disappearing of ester signal.
1. It might have hydrolyzed under the provided conditions (iff acid or base was used).
2. Ester group might have been involved in the cross linking process or transformed into any other.